diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 1552 |
1 files changed, 810 insertions, 742 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 90a0e1f288..47bfa11e68 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1055,13 +1055,13 @@ All datasets are restricted to protein coding genes.") (define-public r-aneufinder (package (name "r-aneufinder") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AneuFinder" version)) (sha256 (base32 - "0m6wphlriq7y21ih1p2kzml5jzcic79jc52kkk59dkjj8j88yllk")))) + "0xn8952fkchhx7m8dam6gjy86j551xp1cs67510s1qrmfgzpkjp0")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -1401,14 +1401,14 @@ across the entire multi-'omics experiment.") (define-public r-biocversion (package (name "r-biocversion") - (version "3.13.1") + (version "3.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocVersion" version)) (sha256 (base32 - "0rsw8g4g1pcjw1zbx8x17yd3drhxqk4sx3cy3ddzy5731hl6mbfi")))) + "0qwzkh2alw7xhjprh719la0lg1q38pmjbipy3s2fy79m4xy8y8ik")))) (properties `((upstream-name . "BiocVersion"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BiocVersion/") @@ -1421,13 +1421,13 @@ of Bioconductor.") (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.38.0") + (version "0.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "1kv7lzmyki3hi771v01nml1v1hzz8pyhqqv0xcdzqy354mlgx4m6")))) + "0nr5x4r8f2krnfrxm7wrzgzr7nbljypi985cbwx5hxhn95zmfifh")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) @@ -1441,13 +1441,13 @@ packages.") (define-public r-coverageview (package (name "r-coverageview") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CoverageView" version)) (sha256 (base32 - "1xhirbjdw09cqm4xvysxqicvqjbahavwvs7shg4cb05gwyd2ha8g")))) + "0sb1h5qsk41c9xisq73agqh502wv6p2j1k45s32a4bkdynf696as")))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) @@ -1468,13 +1468,13 @@ how the coverage distributed across the genome.") (define-public r-cummerbund (package (name "r-cummerbund") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cummeRbund" version)) (sha256 (base32 - "1avvmvrmldbscc7xd6a6k22xjykbzafvqf87wh5z9rx3qlzswsjx")))) + "0130hrlz2jabbshis1g11ndda8b8vlirzi7a004li3cgdghscxql")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -1498,13 +1498,13 @@ used visualizations.") (define-public r-decipher (package (name "r-decipher") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DECIPHER" version)) (sha256 (base32 - "0mr7glkx2d37l9nszs52m0kycpm14vxl5gdp3z7i5j7yig1sw2nk")))) + "0a9k3f70jmd17kxf1zjmdzrfjs0dmwfad2zgz6wihxh5s1shc8qm")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) @@ -1522,13 +1522,13 @@ biological sequences.") (define-public r-deepsnv (package (name "r-deepsnv") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "deepSNV" version)) (sha256 (base32 - "0zz56hf417m7bgg2g2wpbaik30pi6h2nam1n5bviqgdn4mv8n0bs")))) + "1wi6j6yb6i9fs9yszfywqz3w50mhl85dkfmr4w3phwvkf0xkn81w")))) (properties `((upstream-name . "deepSNV"))) (build-system r-build-system) (propagated-inputs @@ -1558,13 +1558,13 @@ bases such as COSMIC.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.18.0") + (version "0.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0w632262dqzcnvq9s6jvc7naz93dayx51fsv05s0zb6cjwygbqjr")))) + "1cm6zh01mvhiq7zrik7q3dmgxinyjz1nyg6rfj93kpkvcb5d4wpj")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) @@ -1591,13 +1591,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-bluster (package (name "r-bluster") - (version "1.2.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bluster" version)) (sha256 (base32 - "128zd5vwlhmrkq0bpp1dxnkrcqfz1mjmdjlla4wqbjv7v6yyn6lg")))) + "1j24l12i3aga4qd827sj8b160yvrhlznggb4piddkmhjc0sppbjm")))) (properties `((upstream-name . "bluster"))) (build-system r-build-system) (propagated-inputs @@ -1621,13 +1621,13 @@ and evaluate clustering results.") (define-public r-ideoviz (package (name "r-ideoviz") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IdeoViz" version)) (sha256 (base32 - "17sx0v5lq2zmg098ps4ksj1h0yla3vlh6s2w1ahqsq0nvm193scm")))) + "0cclk2pcb2mvsfxhw0zq3qlnfkblb1gqxnn7xypmlf0bm6hcvl4g")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -1645,13 +1645,13 @@ arbitrary genomic intervals along chromosomal ideogram.") (define-public r-iranges (package (name "r-iranges") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "0dzj8wqbjzilh2dsaj3ylx958xqrv0c688ayfq2r1z7rs75qy7kx")))) + "07zs231wbfwwc1c1165rhp711fbss40p9l8kyjjv9flzpr3hr1pg")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -1803,14 +1803,14 @@ performing parallel computations on multicore machines.") (define-public r-affy (package (name "r-affy") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "0vz5y92gqcm0qk57qlba85bk683lzdr7vkmxv109rq6i17vdkkrm")))) + "0z66pyn2020h3x22xabkmnjxb20kbgblivvk7mqjk9134wvvf15a")))) (build-system r-build-system) (propagated-inputs `(("r-affyio" ,r-affyio) @@ -1831,14 +1831,14 @@ analysis.") (define-public r-affycomp (package (name "r-affycomp") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 - "07my5scdh6h0y1bx1h9y5m4fa8bnmw389f83gkb7cf19w4vp36b2")))) + "0kawlfff82ikrbrfyyy38zm5wj5xdri2ii9wgwilnq50z5qc6r21")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase))) @@ -1852,14 +1852,14 @@ measures for Affymetrix Oligonucleotide Arrays.") (define-public r-affycompatible (package (name "r-affycompatible") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyCompatible" version)) (sha256 (base32 - "1xwz22wf2smsvmd0d5lfadbsgscnl3fl9msypy2mml38k048p6vj")))) + "1qlfh1gcwa6akd5dhdqh260yaw1j6dap6a15ghwf74rchi5218sg")))) (properties `((upstream-name . "AffyCompatible"))) (build-system r-build-system) @@ -1880,14 +1880,14 @@ Command Console} (AGCC)-compatible sample annotation files.") (define-public r-affycontam (package (name "r-affycontam") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyContam" version)) (sha256 (base32 - "0242ga68wrdk1kcmxfdbq73a0d3zhrzdlzkzphfg3q0zjbvg49jj")))) + "1vw3nxg9jvlw0zg9h70w2ww8l42qpyvgf12hsla9hyyfhj3m6i9f")))) (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs @@ -1905,14 +1905,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.") (define-public r-affycoretools (package (name "r-affycoretools") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 - "1dx861spr3kn1dxwhf43s5l1r7bmrq0h6538l3q64iiwzzc6krdh")))) + "1ccyaj129ii9f47r41qsy34y6ck4wna55j8vz3v3hbldddn93f40")))) (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs @@ -1947,14 +1947,14 @@ to streamline the more common analyses that a Biostatistician might see.") (define-public r-affyio (package (name "r-affyio") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "07kibqsm888g06qqqa4648ph877kriy74kprbri8nyx83y8aspjr")))) + "02lqdq8hcldkf9qbyhhllkm3smpqc51sn2d9gbkm74r96fx37lvm")))) (build-system r-build-system) (propagated-inputs `(("r-zlibbioc" ,r-zlibbioc))) @@ -1971,14 +1971,14 @@ CDF file formats.") (define-public r-affxparser (package (name "r-affxparser") - (version "1.64.1") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affxparser" version)) (sha256 (base32 - "0lr0kmp087j2g4i5kd7rh8a038ymp6z82861lyql2fwk5dh80043")))) + "1bd0f8ifj6l7dx2m3wpmd0mji2gdf39mzgcjf9lbvvmbqnbxbcal")))) (properties `((upstream-name . "affxparser"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/affxparser") @@ -1999,14 +1999,14 @@ structure.") (define-public r-annotate (package (name "r-annotate") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "13ny596wh65sw7dbw0zd4h84d6k1w99g91c4sqy83mdzgpv73sz7")))) + "0p7q5hdk7003q72vg4hrgdzn463spybxhrkvcq3a6l6jkgy9sf84")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -2026,13 +2026,13 @@ microarrays.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.54.1") + (version "1.56.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "0fcammls431pgmp47r85k0zh3bz42bajbqdmafd31kpqncc1ijal")))) + "1svh5zcb7ymz463z5641l2cvzniswxasjjix2plfhqs0yqf1j9qg")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -2056,13 +2056,13 @@ annotation data packages using SQLite data storage.") (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "0799jja6v7l3jsi26wbjalkr5lriaxid05xb5g36iq93myhaj0sa")))) + "15fp1228yb06jm5cblvhw3qv9mlpbjfggaz2nvi3p46mby1vs64w")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) @@ -2082,14 +2082,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "1by3diy0y4809k97cw97mp4j177gn1dzhqil8myij1r7b8sk7hax")))) + "02wvni5q560idi6677g5f4md73z4qzjl5yycxv5dbvgbl2picisz")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -2114,14 +2114,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "3.0.1") + (version "3.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "12i8lafy1z97gs4knqi7r5l1hd7dr6j8a23qj4fkdpqsdpyz21z7")))) + "0ks8yzvvs2r66pb9687mkskf0n3wgvp7h92k83b0a1q32sca5wng")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs @@ -2155,14 +2155,14 @@ by the user, helping with quick and reproducible access.") (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.22.0") + (version "3.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "1yvq6l1p8cpijvlib4fn9y88ihn0gaalrmgx82jgrfmnszkqn3y5")))) + "12qa85hsp8d1xhgn27iymknbhpnp9bd7hsgqxwvp1i8kki06z5hp")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs @@ -2182,14 +2182,14 @@ classes.") (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "1ljrip0jlxjcljqac7vzvwqbcqil5v4f4s4bhpq4akvdkshas6mn")))) + "03m3yaagplh7j4q5hp3cfcdqwsnh1pwrlla9cv3ajnfd83s8ncqv")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -2212,13 +2212,13 @@ paired-end data.") (define-public r-biobase (package (name "r-biobase") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "1sg8w8860zhlz9s1pf75xa8asd2hyqsj13fh5xc37hf5yqdfkavr")))) + "0kar2kgaayp5l7xv9zcxj61l01m8jlwnppql6qf01wsz36dacgww")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) @@ -2234,13 +2234,13 @@ on Bioconductor or which replace R functions.") (define-public r-biomart (package (name "r-biomart") - (version "2.48.3") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "096s243yzbhhz3wsm7azml5sznqczmcpi5g0gnb02mah1przczfx")))) + "069wqihm8pj3r41dizvdbj4jnw9bsc5jrz8czfrak5v69bgk5v5q")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -2272,13 +2272,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.26.2") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1y459cygq21f3igsdlxz1zlyad8qbl2qlr5h2d2dpnvblykvf48i")))) + "0jqgbpjppwinzw100qhc42kc95znq6xanl26bi8m9cq7yggbpra6")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -2306,7 +2306,7 @@ powerful online queries from gene annotation to database mining.") (("\\today") "later")) ;; Initialize the random number generator seed when building. - (substitute* "R/internal_rng_stream.R" + (substitute* "R/rng.R" (("\"L'Ecuyer-CMRG\"\\)" m) (string-append m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n")))))))) @@ -2327,13 +2327,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.60.2") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "0ai0fg0w4l0a7avbafdbqjgjpg91myxalwrg2i3ixm1l2lyyfyah")))) + "11qkw863mkfz3mc55v2gmfr4w3xziqfb5pq3hmjqpn8vpw8ax3xq")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -2355,14 +2355,14 @@ biological sequences or sets of sequences.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "14jyyg3ggdhaqhp0j4qf6dapykh76fygbaa4lr7czqbc5mr0iw23")))) + "0kg71p7sqfvxal0c19zrws1ffaqgyi8p605l3z6mkq5ldi26pajz")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs @@ -2397,13 +2397,13 @@ effort and encourages consistency.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "1jhissp9ad1rn2p0bzr3yslbn84yqbaqgnn5p9hyacwr7mr091cn")))) + "1b023dpy8ygq0kd6qy0mk97c66gzpf39y2s0n89kmv61z5sg0jyi")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) @@ -2428,14 +2428,14 @@ genome data packages and support for efficient SNP representation.") (define-public r-category (package (name "r-category") - (version "2.58.0") + (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "0f76pb7h8qc51mca5pq00m9p02sbkcj6ywfzli20qai2ykpfr71x")))) + "164zp4la9rqnp5vpn2y2p6plc5yxyk2kmn0z3d2flla54zc1b427")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs @@ -2459,13 +2459,13 @@ analysis.") (define-public r-chipseeker (package (name "r-chipseeker") - (version "1.28.3") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPseeker" version)) (sha256 (base32 - "18hdgml80770c0xgd06zrl8px1ql9fa65rirfkq07z7rzpnd23rw")))) + "1x8px8ylc231g87rd48kmy9y36h26rldbmqjkcj4mgaldvbsj0rp")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -2506,14 +2506,14 @@ annotation, distance to TSS, and overlap of peaks or genes.") (define-public r-chipseq (package (name "r-chipseq") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "078p9h0zghlhpd6cr54nww1mk7q97imx8yqfayw5m2yq4097ivbi")))) + "1jw209bfh1c22mqs9z44qx3pmca9m68rhxp0p9bvbmqsnqwrndi6")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -2532,20 +2532,19 @@ experiments.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "0jl96msj1njdrvngg68s50vmphvhi2lfwlv34x07pcdzgkjjs41f")))) + "124w74mk0zk035wyr7cimblzx5blags4n5c8f83mp7iimxcb4gcn")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) (propagated-inputs - `(("r-cairo" ,r-cairo) - ("r-circlize" ,r-circlize) + `(("r-circlize" ,r-circlize) ("r-clue" ,r-clue) ("r-colorspace" ,r-colorspace) ("r-digest" ,r-digest) @@ -2572,14 +2571,14 @@ self-defined annotation graphics.") (define-public r-copywriter (package (name "r-copywriter") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "0pacs714d9b1fdz68pp9ca0x77d376s19lxb82np4l9fgx0rgkxp")))) + "0xm5gjzi4r1xzyn7r669blqxhyhmbk9rh9k2gn696j14hbhc1hcy")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs @@ -2643,14 +2642,14 @@ distribution.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "0r1brwmj7av0bj72jajn27vx3zs1bgg8qfbhf02fln6kf7im4kaz")))) + "0whk29zrmv9mrlc4w5ghy0fd29v8hfr8jccwgrn59mf3mkmfb2b9")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs @@ -2681,14 +2680,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "1zywh30f4j4rj0f9w6yk5xr9mvdbg8gicy3wsb8yxdnamadyr7x4")))) + "1wd4bjd0a53s689yvb2lxzdiy0synh6ncfcly3cfw37kpdj8lds1")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -2726,14 +2725,14 @@ exploration of the results.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "0ikmj0300lfzj6q1vyahfyx5kwi5h59mds7ym4f2j1bbxqzy6ssl")))) + "06nallp9jj2vmaa7d18g6hiymjc109szdv8sp51r87n7s38bvyq6")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) @@ -2755,14 +2754,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-edaseq (package (name "r-edaseq") - (version "2.26.1") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "0pakcbkalhhqz3d9lpfx3hscf53k24mlmrywxxzfg43yq57srkql")))) + "1vygfdxbjcww7sqzc3j7sp7w13dx10vlzy9z31flf7345qp6blj7")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs @@ -2795,13 +2794,13 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "3.34.1") + (version "3.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "0f6apsjq6cn794840ls9y2n0hix1gyhvkdgxch1v22qr4sq0c86k")))) + "1d18kdfi9vjhhw5kwfy5airrd3c16fh4wbwppbhwgawm038mwavk")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -2823,14 +2822,14 @@ CAGE.") (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.16.4") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "15yllkxr6sj5pfvkvv285nk3q5374nzq1iz8ywmnrq910k3xagd8")))) + "02rdbqp33g488w1df1rgp0dg63qrr6w2kmgigxzc8l9wmrvj0y1j")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -2868,14 +2867,14 @@ chromosome region or transcript models of lincRNA genes.") (define-public r-fastseg (package (name "r-fastseg") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "006v7qs707xmnr35b7rw135pyvacrmhv55a3c53birkpsrjgkps0")))) + "1ds0hhc41nhfj3lmvld8nk2p547wd80b3yq7fjlf3dl3wfaxzy80")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -2898,14 +2897,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "0z7hrwdm6my6p7z04bcpfhqk72pd0s1bdzvsiiym59qj79fbvb83")))) + "1spndmvl8wlz3z3wsvzi0fg9nzk81xi8c220pg2rf81j9181nkar")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -2929,14 +2928,14 @@ analysis using other methods.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "0dy9pmlb0pc9b4ks5fb9zgnmhc9f2mkqmsdlb7f5z88xmj68y4qk")))) + "05ba33m99dg414lasn36mjmkd9lvrxgpamy1qj2zvi31i9vkq6y2")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran) @@ -2957,13 +2956,13 @@ high-throughput sequencing experiments.") (define-public r-geneoverlap (package (name "r-geneoverlap") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GeneOverlap" version)) (sha256 (base32 - "1kfw3h68rvbafhklds6sfmviwv91nms8wk0ywzkjg5h3mmgxbsv9")))) + "18l5dc4xcy1xa2h3sfw92w9rq9v0mnclamjxmzs5fqi469y5mwmm")))) (build-system r-build-system) (propagated-inputs `(("r-rcolorbrewer" ,r-rcolorbrewer) @@ -2977,13 +2976,13 @@ and visualize the results.") (define-public r-genomation (package (name "r-genomation") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "0qa3b4mfd7l1sy4pw64zr2d90y5apah900krxjl4x39acygg0i2r")))) + "0ynwsrlnp98iyz4bl2s7plin0k9iy9zix4jy4v38lcqg6n4iz00j")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) @@ -3024,13 +3023,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.28.4") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "0fjpgvpvyvl8cqgh2annib6h0c5li3aqz1ajfh5z5k5d0avdm4w0")))) + "1r0wblz9w4hqxm15wdssz0invx7hxhg3bnblkia6w3aazh30s6ns")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -3054,13 +3053,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "00rq110jkh89nxgk05zh8kssxk8mb4dq0wjg3n7ivfmmm9wdwhp2")))) + "1jwksis94mk8bmdggk0w3kvxqwp4di6x78xgsjk6ij54710adyq9")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -3087,13 +3086,13 @@ alignments.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.44.2") + (version "1.46.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "091p8xnf2xkqhind81vyv1rmy2fz2b3qalcbrsw4qnp24vgdv2am")))) + "1dm049r7k41m8zzp5b332fw3ah3jpzzgpcb21icxwhlg483ipjyv")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -3131,14 +3130,14 @@ extracting the desired features in a convenient format.") (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "1plh14m7w6calw5yxcxp7g4bg8q00ax85m517wap78bni975k13y")))) + "0i5y6dk6z18yqj5k4zy756c6l57z9jq2w5a5dksh2di4qgdgjx3x")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs @@ -3165,13 +3164,13 @@ provide added flexibility for data combination and manipulation.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "1qxc6dcwdlkan3hg0j9yfhz7gyi9qg671yj6zizsk6mzl7qqva0x")))) + "03fdmzcf8h17ksa3byc3k5mxc65pqrbcnw00myz1q53l01p3cnf2")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -3196,14 +3195,14 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-gostats (package (name "r-gostats") - (version "2.58.0") + (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "0jjswy6qmfgr2f6vk3y9pdvs9x91gn31h55qllgh0qb2cb26g9wa")))) + "1f8wqdl0swnvs59i6ljjcaglfqv314n8zxy4crpx806gbjzpn76z")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs @@ -3227,14 +3226,14 @@ testing and other simple calculations.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "0946kkykms79mqnx262q20xzrrhv7cv723xh378335ff41qyf63n")))) + "1i8rryvagxk2pd8nl4a6yldwv82yx869nvv95jf8v00bna08f4d6")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs @@ -3256,14 +3255,14 @@ Enrichment Analysis} (GSEA).") (define-public r-hpar (package (name "r-hpar") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "0q5pp04rq2gsh1kibvp8bvjkqc1kb46qpnj6agqp2vyqhrrfrm99")))) + "1inajapdhjxg0vwhsdnhfq22h3fv7ad7m1lv58y5v41p59av1w76")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -3276,14 +3275,14 @@ the Human Protein Atlas project.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "0acpgv98529ic2i2k03knz05akb6h51wbz7sr5zgi8gk4nmawrlf")))) + "0pwmzwjf6agfp3bq6w8s3piwmzwjdd474qd8zmbzrm772qbadfr4")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, @@ -3307,13 +3306,13 @@ of other R packages who wish to make use of HTSlib.") (define-public r-impute (package (name "r-impute") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "0pprkv25avxhllddcssvqvy3nibmqkfwaq4xnlhka7858gyiyd1k")))) + "0k6dil8ljgp5qr87m7hxli4igb36fbxiwczaqc5pi8mlfh70fqj5")))) (native-inputs `(("gfortran" ,gfortran))) (build-system r-build-system) @@ -3327,14 +3326,14 @@ microarray data, using nearest neighbor averaging.") (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "00rgrrmglslgb6j7whp0m5dlyl4436r647br05rrpv8cxrmbs2iv")))) + "1pi887192k1jifb4k3pf2jn5hcl1xmmy6vwl22r9njsprdyb3kab")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) @@ -3354,14 +3353,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "15313d20v3ziyn52fhc6fbzcy1kxjkdx18124bxhdfd14f4aypcd")))) + "1np3i1k7rki9akh70156ggmid52yy0is9q5vd3s45ra7an0ap279")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs @@ -3380,13 +3379,13 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-limma (package (name "r-limma") - (version "3.48.3") + (version "3.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "0385ac0hvvml99krcgcpp6q7layjhzgp9xcxkcjrpfg5mjg1z4sx")))) + "05ypmax1s6y1nz42bxn61wxhzzw6185q633crzpdcbbz3dz4vgvy")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -3399,13 +3398,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "147nag4rz2xpjkkf8rmhja9k4ixjj1hsb0lq3lw7mw6q67zxsvf3")))) + "02px46h2ynprss7kwll3i0jz0clrdg0bys70jacd432xw34nm2sx")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs @@ -3473,14 +3472,14 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "3.2.0") + (version "3.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "0433i4xbz8hrfaj8fxgzps3x8dqrl5vgwzg7qmp4cy5sb1lw5wvs")))) + "1n9rakj57yf17hay1bzvwc2h761yijmlflb3crg1bzwvmn32yhsl")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -3503,6 +3502,7 @@ throughput genetic sequencing data sets using regression methods.") ("r-nmf" ,r-nmf) ("r-pracma" ,r-pracma) ("r-purrr" ,r-purrr) + ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-s4vectors" ,r-s4vectors) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) @@ -3518,14 +3518,14 @@ in SNV base substitution data.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "1z7s17j6zgb70m0khyf9icqlnbnzlivca7vw7j0vxyw417ld9lkr")))) + "1r5igzb7xb5qcw37ffy0c3j6vlg9zffmksrc57rs1pmfnca773z5")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -3563,14 +3563,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "0r3vgigf4fk0xzfg8gcvad01jdh0fysh6x22m9qy77x6glyrxcj2")))) + "0dks5h3vp9ly8x24px2rl5blqicxybpxjnxvg2p1bwq8zvjkm38p")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (arguments @@ -3620,14 +3620,14 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-mzid (package (name "r-mzid") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "1wsy6frxa5602jqb1nlqv39mzgpid8wfyvb9m2jb6srv7p59rgys")))) + "0r001amd4m99cv0ixw38rpz0zv0xqb0qyvs16bz1i4a756391qri")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs @@ -3651,14 +3651,14 @@ specific parser.") (define-public r-mzr (package (name "r-mzr") - (version "2.26.1") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "0z4cz6lir9gwzy0hxwv03wv36fkkfdb97p9wv4af020k0zkp3ipr")) + "1azq0wjjy6n5xc721gjz6afm43ajz15b4p34vgsdjzwg9qn1vrs1")) (modules '((guix build utils))) (snippet '(begin @@ -3681,7 +3681,7 @@ specific parser.") #t))))) (inputs `(;; Our default boost package won't work here, unfortunately, even with - ;; mzR version 2.26.1. + ;; mzR version 2.28.0. ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources ("zlib" ,zlib))) (propagated-inputs @@ -3708,14 +3708,14 @@ previously been used in XCMS.") (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "0p8ccpdchdwci4kv9y07wdadzgms8nipvg6rm1rll35jcflnnkxi")))) + "0zp6x2iqhn9s3xp07yilnr6hn73acvkdai5xip4iiwjdlnfffj83")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs @@ -3740,14 +3740,14 @@ the fact that each of these packages implements a select methods.") (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.84.0") + (version "1.86.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "1ccqsxn487dy92c2d1iffh9917z4zq5ia92zv2h6pi00jjc6ymb5")))) + "1fj2v6sna4lbw7ar9h93y2g4pzylqqp7760ih425gcai7s19xdrg")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs @@ -3770,14 +3770,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-protgenerics (package (name "r-protgenerics") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "1c79k8nc28782w5gxi7pkm8jmddq1hdw6khs9kgsp8dyk60ak6fq")))) + "0x53pk7h47gjza1q5pz7jb1qqhwa9z2rr5fr61qc92zl3mqk57m0")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") @@ -3790,14 +3790,14 @@ proteomics packages.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "0l40ibf8g5s4ay83s92l198jjqc5l09hcmxqcjrpifvp5pjf9yy5")))) + "0k2p1lwdvix4n742a97lv988rx5kg8cvcmzgyzj0538n1nz0lxk0")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs @@ -3813,13 +3813,13 @@ the graph algorithms contained in the Boost library.") (define-public r-rcas (package (name "r-rcas") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "0l92v870ndna8zjqwzf22fb9vyhkh6942v4gaiqr1yc4qr521p5p")))) + "02zwz7c8ljmdcfxj54xns0a31sj616x63q63wxhxa1nb4dhgmvk7")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs @@ -3863,14 +3863,14 @@ library implementing most of the pipeline's features.") (define-public r-regioner (package (name "r-regioner") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "0xzzaz3cl6pyxfsg0d931v8k15wbd05s5mnsb7igxldc5qqg3nsl")))) + "0y1mawzfvxrympc47q3isk96sl9d1bc8kdsxpm8rnhqg5bmgwya6")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs @@ -3894,14 +3894,14 @@ region sets and other genomic features.") (define-public r-reportingtools (package (name "r-reportingtools") - (version "2.32.1") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 - "0wq9y649dh1am6djzz0xlz42428xsgw2bdx1dknhdw2xbydmmx47")))) + "06kwf87h84xgswkrm7brmgr9aj1nf6cxp24hrfymkzq2pha5y5j7")))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) @@ -3944,13 +3944,13 @@ browser.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "1a5kw9ry9cr258al0x3q0ss5xn1ymscdypx51vzzgzamhy7dqakz")))) + "13zm993l3i9f98gqdpxgsrzf9fgqppx2ajvrl0i3f7cvpifcgxqg")))) (build-system r-build-system) (propagated-inputs `(("r-rhdf5filters" ,r-rhdf5filters) @@ -3972,14 +3972,14 @@ the available RAM.") (define-public r-rhdf5filters (package (name "r-rhdf5filters") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5filters" version)) (sha256 (base32 - "133v0s452acspi4dbf6gsa2xrr0qza86jdjjbpwhdv6zfd1djbgc")))) + "05b015pyp3g1crmm2d3ldsa7r5w0khmf87qbl4fv16r6pdggha78")))) (properties `((upstream-name . "rhdf5filters"))) (build-system r-build-system) (propagated-inputs @@ -3998,13 +3998,13 @@ HDF5 datasets.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "0arhh5bbx3pmxmkh5sjgczcswqy83d35r7cjhd2knpczdvrixaq5")))) + "0v6b3j45ivd9f04fpfs1vjwby5pi30mf5683bjxim01vi2krj9yh")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -4067,13 +4067,13 @@ tab-delimited (tabix) files.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.52.1") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "11w6dx09pb49lin1gr9q88xn7ixh9jd5z6m9z27djchm0nw10lx9")))) + "11bh9khra2qdmicppi6ya43kf8f1z13ak92vkl6nr5f20k54cphc")))) (build-system r-build-system) (arguments `(#:phases @@ -4146,14 +4146,14 @@ differential expression analysis, RNAseq data and related problems.") (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "1253sj1hc6bbrff0iv5xa3v9znqvisll0fy6fdjka9c778fn4mcp")))) + "013hwj2lp29nqa8mkvm25aliarg0k725crg4cpsbj0iiskyrs6rl")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (native-inputs @@ -4169,13 +4169,13 @@ Stephens (1990).") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "0h74z84zyvfzclsm0g13b95hirn99185wc6lp53jkzah9yyi59ay")))) + "1mik575qaxw9h9qyjn971207pfgbc8p1mx60jrb20jbrrihgg2na")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) @@ -4196,14 +4196,14 @@ reference point and sorted by a user defined feature.") (define-public r-shortread (package (name "r-shortread") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "0zqinw3c6h5v1c5nhzkiziirws16nbviccgw8nj2d22r33dbqwp3")))) + "1p17v15wd3v6w9ligpjjk28vy8k2ql57y2hhm8y6vnv9y3nagjsx")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs @@ -4239,14 +4239,14 @@ ungapped alignment formats.") (define-public r-simplifyenrichment (package (name "r-simplifyenrichment") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "simplifyEnrichment" version)) (sha256 (base32 - "0rqa414kvyjjmj4932zk39rqa14z13b57rkrxdrf16jmq2r437vh")))) + "05d9yjd8s7q1q78qmnx5xfrz9ppswc2cpfmjj47d338w783lwk98")))) (properties `((upstream-name . "simplifyEnrichment"))) (build-system r-build-system) @@ -4278,14 +4278,14 @@ and comparing the clusterings.") (define-public r-trajectoryutils (package (name "r-trajectoryutils") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TrajectoryUtils" version)) (sha256 (base32 - "1b7mg3ypp1ay98cav47h9vn692lx0n9b5b0hpansgnkr5prb823b")))) + "0pzm1h69bg04a2v09r8c6pb3pix6f3n5dylvbv7wsp574qfaqyd1")))) (properties `((upstream-name . "TrajectoryUtils"))) (build-system r-build-system) @@ -4308,13 +4308,13 @@ structures to hold pseudotime inference results.") (define-public r-slingshot (package (name "r-slingshot") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "slingshot" version)) (sha256 (base32 - "1aqsz2kxwax8d8d5iv3zk5hlyk5aya1wbxs1wky2rgccw4d35whx")))) + "081kp9b0lpw2xq9xvd2kykqqrqcj322mp7xa44xc3kf0nzsivqfa")))) (build-system r-build-system) (propagated-inputs `(("r-igraph" ,r-igraph) @@ -4340,13 +4340,13 @@ graph construction.") (define-public r-structuralvariantannotation (package (name "r-structuralvariantannotation") - (version "1.8.2") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "StructuralVariantAnnotation" version)) (sha256 - (base32 "04ac4mjh3pgdlws0aiacqg0vd7bhg890w44r7b90p947c3rk1mfw")))) + (base32 "1pw7d39944dwk5gw6q7igcn866zpqwz01ljaha2ih5dfvmhxka8n")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -4377,13 +4377,13 @@ involving two separate genomic loci encoded as GRanges objects.") (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "16np5ik6jgbi68mhlib6yskywwbaa50mlr7m3sh1hqk889whfn1g")))) + "0qpnx2aii9vs7fcp0ax5j77ysbhi4qhjhm35vnygs3isbrjn925a")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -4411,14 +4411,14 @@ samples.") (define-public r-sva (package (name "r-sva") - (version "3.40.0") + (version "3.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "12jkcybdfspabh7x124d44l9fj1hwwg3gvcqxvz5wpkiflc2vkji")))) + "0clzid9di2qfgc5bvnqx312k3inj1lc599ckqkllvr894wxb7mdj")))) (build-system r-build-system) (propagated-inputs `(("r-edger" ,r-edger) @@ -4442,44 +4442,30 @@ unmodeled, or latent sources of noise.") (define-public r-systempiper (package (name "r-systempiper") - (version "1.26.3") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "01l35l5zj87qkarrbal9la6kshk3j7k8hy3iimv3gdnnz4axmvs7")))) + "0kibr47z7ml13hpl955qcr4wp2z4nq7gjiinyk30wivrwrng5sg1")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-assertthat" ,r-assertthat) - ("r-batchtools" ,r-batchtools) + `(("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) ("r-crayon" ,r-crayon) - ("r-deseq2" ,r-deseq2) - ("r-dot" ,r-dot) - ("r-edger" ,r-edger) - ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) - ("r-go-db" ,r-go-db) - ("r-gostats" ,r-gostats) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) + ("r-htmlwidgets" ,r-htmlwidgets) ("r-magrittr" ,r-magrittr) - ("r-pheatmap" ,r-pheatmap) - ("r-rjson" ,r-rjson) ("r-rsamtools" ,r-rsamtools) - ("r-rsvg" ,r-rsvg) ("r-s4vectors" ,r-s4vectors) ("r-shortread" ,r-shortread) ("r-stringr" ,r-stringr) ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-testthat" ,r-testthat) - ("r-yaml" ,r-yaml) - ("r-variantannotation" ,r-variantannotation))) + ("r-yaml" ,r-yaml))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/tgirke/systemPipeR") @@ -4499,13 +4485,13 @@ annotation infrastructure.") (define-public r-topgo (package (name "r-topgo") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "1ggi7yrhkyi85p3sfj3yd95n9mzq1xpff28ixa4dl9yzasks1v5a")))) + "01vykf8bzwm2k7cfj09r6il6qaycjy10wpaxbn13f21p66r5nlm2")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) @@ -4532,13 +4518,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-tximport (package (name "r-tximport") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "0ip2yr0zspf2aagskxl4dwncr48dw5qb90an3sswnnh2dqdb82if")))) + "0w6pr7s9j8l4fpn3przbfrsyxvzxc3ficgsychvhq3bami9np8g4")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -4556,13 +4542,13 @@ of gene-level counts.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "0c9r00j8a3bs6n0dv4wi17jc1ljzvr3r2bi4h9axhcsf2ip906rh")))) + "1r9kayp0hxcwls08lv2fh0cmf9ks0lqx3k31c1zn4asw4dyqpgva")))) (properties `((upstream-name . "VariantAnnotation"))) (propagated-inputs @@ -4594,14 +4580,14 @@ coding changes and predict coding outcomes.") (define-public r-vsn (package (name "r-vsn") - (version "3.60.0") + (version "3.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "0nppph3kv8z83368snb8s3n4vcqj829yyi1kh4q09qvq18rhvssv")))) + "03p2wdjbjnrn1ddyz0fbn04mdxpsmv83qhh3apj6azshl0bs1j2x")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -4630,13 +4616,13 @@ and specific in detecting differential transcription.") (define-public r-xvector (package (name "r-xvector") - (version "0.32.0") + (version "0.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "1cw34gd9iaspl0v737xl7rngq63zrj03a5ngai15ggrnv1sq2aqr")))) + "07r4qgmnifw9jk2srjg0cvl310j0f9y35jrg0zqhlvhmyhg6n2c0")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) @@ -4666,13 +4652,13 @@ and specific in detecting differential transcription.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "1dv5bf12kzk1yzyfs3g5syim16sbi44kalvzj2i2xcnxnl6x60ip")))) + "0a0dl7z58zxdj6938zbxixphgljj1giylk1nd05bb7qsccmp0xhj")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) @@ -4682,17 +4668,49 @@ and specific in detecting differential transcription.") libraries for systems that do not have these available via other means.") (license license:artistic2.0))) +(define-public r-zellkonverter + (package + (name "r-zellkonverter") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "zellkonverter" version)) + (sha256 + (base32 "1ihp2f23lpdfgf3qliy22vrq8czm353hyhqf74r5r712190k6pgg")))) + (properties `((upstream-name . "zellkonverter"))) + (build-system r-build-system) + (propagated-inputs + `(("r-basilisk" ,r-basilisk) + ("r-cli" ,r-cli) + ("r-delayedarray" ,r-delayedarray) + ("r-matrix" ,r-matrix) + ("r-reticulate" ,r-reticulate) + ("r-s4vectors" ,r-s4vectors) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/theislab/zellkonverter") + (synopsis "Conversion between AnnData and single-cell experiments objects") + (description + "This package provides methods to convert between Python AnnData objects +and SingleCellExperiment objects. These are primarily intended for use by +downstream Bioconductor packages that wrap Python methods for single-cell data +analysis. It also includes functions to read and write H5AD files used for +saving AnnData objects to disk.") + (license license:expat))) + (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "1d085lfa3yif5wkys1fb0zzgg0cqwd1y18vasgqqdr6rva075d4z")))) + "1b7ngp9l00vrymx3d3nsda546s7p4ifr90idn3x2v4ilf38rfhp8")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) @@ -4710,14 +4728,14 @@ libraries for systems that do not have these available via other means.") (define-public r-oligoclasses (package (name "r-oligoclasses") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligoClasses" version)) (sha256 (base32 - "1nsfyfpj264h6y322pzz0i001b0m862j3skbq5rjwlrj1p8j2gi7")))) + "1ia2f19swiwb0552nfwkai4gl0av07cj75b6jwiviqa1bli09264")))) (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs @@ -4745,14 +4763,14 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "0fyq77im6s79havjwbchhqhnllxs134jsi98g6msxz66h16lj3al")))) + "1cmnnq0d5xsjsx8c8n8wcl6l9d31sbglb8yrsibykcvnhw15fsf6")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -4781,14 +4799,14 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") (define-public r-qvalue (package (name "r-qvalue") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "0xssanffh1hr7f48mnazcpwi25rdp7mxlyb9nbf4q2mp7m40jnpm")))) + "1mn2qmqn89lfsx7rg54d1lwz45bfx0b91q6ahf43a1yzrrhwn138")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -4836,13 +4854,13 @@ integration with @code{Rcpp}.") (define-public r-apeglm (package (name "r-apeglm") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "apeglm" version)) (sha256 (base32 - "1xld6ar440achik4dbd7vhiw6jfj0sb96jm52n7hav5bv4gag3mh")))) + "11w4vyc1sllmm5lh42krhidazid78n4s3lhikpy9kk2l57jmifbr")))) (properties `((upstream-name . "apeglm"))) (build-system r-build-system) (propagated-inputs @@ -4863,13 +4881,13 @@ posterior for individual coefficients.") (define-public r-greylistchip (package (name "r-greylistchip") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GreyListChIP" version)) (sha256 (base32 - "1g9ja8p90czx83ar0l9ran7m6aggvszdbqm714fq7z4rxq9b4hs3")))) + "1h7h27q6l9d8j0shklyrh135zrwx56v4zzmm21cj1b7dvmwvpbcv")))) (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs @@ -4890,14 +4908,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.2.7") + (version "3.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "01jfxcj5c0088vvsi3pz8fs0ka6n12l2j8s1d0rpqwa1y0444x7z")))) + "15p4jd9k520va6kzizkgsl4a18kh5r8i50qfdkv7xazsfhvxjm3i")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs @@ -4968,13 +4986,13 @@ processing to visualization and annotation.") (define-public r-mbkmeans (package (name "r-mbkmeans") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mbkmeans" version)) (sha256 (base32 - "1k7ngpx4s50jplrsv19zzjr7izpdl9wwppb218ih5cp0ki1gcc2n")))) + "03hpj218s8fynmk1s50s0rinhsljikxdrff06yc8ysbyc6hyfb4k")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -5000,14 +5018,14 @@ large datasets, including support for on-disk data representation.") (define-public r-multtest (package (name "r-multtest") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 - "1wi15v4llgv11hpb2j9h4a35nrnawnmvbz5d5dvgy8lhqrlq8w9a")))) + "03z71r7g318nwwgiz0k8qwbhghw1hhdhh1an4qnb0nc62c5x9kns")))) (build-system r-build-system) (propagated-inputs `(("r-survival" ,r-survival) @@ -5038,13 +5056,13 @@ expressed genes in DNA microarray experiments.") (define-public r-graph (package (name "r-graph") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "1i7s198d5kw4gk6nqqsd3vqaknj4493p822f2za8q95gv6x02rxa")))) + "0x31lz3qimxmng6w99xnqazaj943d94b04nbziad4jfv7c1bc2h0")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics))) @@ -5136,14 +5154,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.26.4") + (version "3.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "1iqzm7pifl9zrw3s06i6h85n1p01pd06vh1a93izyfhgybxn262d")))) + "05fbq8zvww1nlyykrri0hf4248i1i7w5cr453giagmjq7lgg4v3b")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -5190,13 +5208,13 @@ enrichedGO (addGeneIDs).") (define-public r-matrixgenerics (package (name "r-matrixgenerics") - (version "1.4.3") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MatrixGenerics" version)) (sha256 (base32 - "1yir3rwhz5vf0pdn3fpvlc57c75k98gvv8gapajbvymz3lyghijv")))) + "1s75p8rrmj24r0vcbaiyw8xg8y84j388mv6iawai7pypfcl8s1z3")))) (properties `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) @@ -5217,12 +5235,12 @@ incompatibilities.") (define-public r-marray (package (name "r-marray") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "0wpmrhqpyv27h1hn31hzz21r74r7yqx79ljv8i8gn6ix8lf5ca56")))) + (base32 "1la805y8j522vpiazm1z6wpq4ibia9bib5fpiia5mxmpzmqg6gzz")))) (build-system r-build-system) (propagated-inputs `(("r-limma" ,r-limma))) @@ -5236,12 +5254,12 @@ normalization and quality checking.") (define-public r-cghbase (package (name "r-cghbase") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "1p87k4vw981k97d9bckmprrfg55jwd91658rgxzjj8hnschf28a4")))) + (base32 "1kfxw126bddfy67cmf8dca9qq4bg7fkxjf8iaikplhvs5hl7bp4d")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs @@ -5256,12 +5274,12 @@ the @code{arrayCGH} packages.") (define-public r-cghcall (package (name "r-cghcall") - (version "2.54.0") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "1zik04y2q0anzy85l0b4ryzkxpfx2fnmpwp5s7akyk1jfl2r8gw7")))) + (base32 "1r4y8zakgmdbnpwgp14kwh4iwqgqcmjq2yg4nc7j37p09bw1c8zr")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs @@ -5279,12 +5297,12 @@ the @code{arrayCGH} packages.") (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "1p4544xlarkbgs9kybrrawq3v7qr6ix62nrc6l7dcksh2ka69yzf")))) + (base32 "1sza9br8agpdz1k9fn5wisir44sj8v0rk4wbx35d2c2kp9q70pqj")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs @@ -5292,7 +5310,6 @@ the @code{arrayCGH} packages.") ("r-cghbase" ,r-cghbase) ("r-cghcall" ,r-cghcall) ("r-dnacopy" ,r-dnacopy) - ("r-future" ,r-future) ("r-future-apply" ,r-future-apply) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) @@ -5312,14 +5329,14 @@ respectively.") (define-public r-bayseq (package (name "r-bayseq") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 - "0hyc0sl2nf18bz0jxbzim0v41zwh2rnnr7l3p6zkk9wnw5gn7bbc")))) + "1zgxwb287ccz4wqsjxmffknnzziv12l4yrw7df912dxz6yccvd8r")))) (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs @@ -5338,14 +5355,14 @@ more complex hypotheses) via empirical Bayesian methods.") (define-public r-chipcomp (package (name "r-chipcomp") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 - "1kfxjh1mynrgqsy2q6byf03cbymqc8w7l7672iyd0wj5qzlif4h5")))) + "1wdy92y5l3wa3zgg59w69rd7gdwf4z1waa4i2cccniccz463p1xq")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs @@ -5372,14 +5389,14 @@ datasets.") (define-public r-riboprofiling (package (name "r-riboprofiling") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 - "1jmd8yrv7p7hn4gdibg3svmhqxjyrnfp7cgsqg8zv862lgd75zsl")))) + "1szlzvm8ggjc40k4z2fxxa2h28g6j9wj2g5aw480v9hgyvvdw5lx")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs @@ -5413,14 +5430,14 @@ assessment, principal component analysis on codon coverage.") (define-public r-riboseqr (package (name "r-riboseqr") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 - "1m5w2j35wr0lzwir4s58z757vrcsj5mglsqrkvs241k0hlmn06qa")))) + "0nnhjvjl4c9yyfzjf8kcj4yky5cdimicp7lz008sczy19jq4vjhd")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs @@ -5441,14 +5458,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (define-public r-interactionset (package (name "r-interactionset") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "034xidjmn67n1471fnpdmz7gjm6p05cj8sp9nssc3gxdzn54a6xb")))) + "19m2mpby73zanai68rlqvzx9zccli4dz4kix93acrw9755xp3bsw")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) @@ -5475,14 +5492,14 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "0zjl7rp5fk14kqsx0bkbpq6hqahbkiyvwa9aggp4kfb8hnmz9qal")))) + "090kxq5jn1jfr9fgbkvbjr5g4bcxzgsaal3gc9yx1n7pgmhccfmb")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) @@ -5516,14 +5533,14 @@ information and producing various plots and statistics.") (define-public r-ctc (package (name "r-ctc") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 - "1v8aysvy6a3r1iafc3xvk885c128kb3pb9zpcdhdjcn0by96k8hh")))) + "1yq5igwzcwfhxy49qf3pralpikiqq7sqr1cig8mkpjpaj5bbaayx")))) (build-system r-build-system) (propagated-inputs `(("r-amap" ,r-amap))) (home-page "https://bioconductor.org/packages/ctc/") @@ -5536,14 +5553,14 @@ trees and clusters to other programs.") (define-public r-goseq (package (name "r-goseq") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "07qrxssx4rb8r958r1smx8xfpzdxpp55hci3201hcmz3mxz77i0s")))) + "1psl9mqgx1d21kayaxvrxriw34fq30wnd57q5c1sk3p8iahg73g0")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -5562,14 +5579,14 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "2.2.0") + (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "0dsk8qmwimzmd1x4k4jwg9q11jm1ahn8cw0gzd6s2gmigfls4hsa")))) + "0qkbx9n2vb7kvb5f00csnbffy5bm7hhbdvkx2isgzi0wv0y59kx9")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs @@ -5595,14 +5612,14 @@ information.") (define-public r-rots (package (name "r-rots") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "18wyi73l95df182vg3m014sxwdbpggr61vsbazhyw4vyx2fnzmpl")))) + "0qhy984y83a3nf4zw54rasw3vn932q4zb3gljifkw701jnrzqmki")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs @@ -5619,14 +5636,14 @@ in omics data.") (define-public r-plgem (package (name "r-plgem") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plgem" version)) (sha256 (base32 - "1rz5jk5bgpk7gjknx79jyslahjg46q2f4bx6dgd0vwmarc29a45z")))) + "06w8xlw4j1fc9ipdgw55dvhp07f04icmhr20lqzwwhqd5pskrra3")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -5644,14 +5661,14 @@ genes or proteins in these datasets.") (define-public r-inspect (package (name "r-inspect") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "0jh5db9dv5pb6b50sg22x8q55m3h0h0nkmb9mivvvp22dhyrd82z")))) + "072kv5k3giyll1clzrg0anqhyl4qbi7cjnmkqz25zdl5bab9l7jk")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs @@ -5691,14 +5708,14 @@ modeling the rates that determines changes in mature mRNA levels.") (define-public r-dnabarcodes (package (name "r-dnabarcodes") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 - "1wiqmzjcb7flp7ldcgbx91asxxrmm1rg9pcfljniab9xcsldhksp")))) + "07yaz98r18mjny1ilmfnjxcra7xpklnd183pw0kasvsri01ccwxg")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs @@ -5720,14 +5737,14 @@ demultiplexed, i.e. assigned to their original reference barcode.") (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "1fy0k1p0m209lzjpd5jhfnifa22lrn63qq3a3kn5g0xhbbmijzac")))) + "1a19klscykdgsd7izcxyr45ml7g0gpdj65gvbaw124mal2p4zi9q")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs @@ -5748,14 +5765,14 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "0cjidi18wjip9xzx83890wjk40vvjq06prf1ag4m2kac47w01r7v")))) + "04in8l6j7frgm0a5dzphazfhn9cm8w775z5yir712jxa37mh1agr")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs @@ -5780,14 +5797,14 @@ achieved for all methods using the BiocParallel framework.") (define-public r-scaledmatrix (package (name "r-scaledmatrix") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ScaledMatrix" version)) (sha256 (base32 - "1j96fvw1waqxbv5c8myfmhsidq370z03yz13yqmrs4nn1rpn1a06")))) + "0vz8441gl5gycy1ypybwhq97bnyvhhlg6gxpi1dsdy2c9b6d81kc")))) (properties `((upstream-name . "ScaledMatrix"))) (build-system r-build-system) (propagated-inputs @@ -5808,14 +5825,14 @@ multiplication.") (define-public r-treeio (package (name "r-treeio") - (version "1.16.2") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "treeio" version)) (sha256 (base32 - "1y60yvg1rl21cab9xrkns0209pg44mwr90qj099dvk97wsjkx67g")))) + "03gz378qrp6b9fcriqanfnphibqv4bxhvz48rigzkidkzz71wfaj")))) (properties `((upstream-name . "treeio"))) (build-system r-build-system) (propagated-inputs @@ -5840,14 +5857,14 @@ platform for merging tree with associated data and converting file formats.") (define-public r-ggtree (package (name "r-ggtree") - (version "3.0.4") + (version "3.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggtree" version)) (sha256 (base32 - "0xf4b9vfdyzzivwgw4ymapl5bb4k9p04mmr53822kxgfd5qrs1zx")))) + "1c6b7kjh44k096v8mhn53abr181vpbn7s6ab7zk4phnsyfxsclxb")))) (properties `((upstream-name . "ggtree"))) (build-system r-build-system) (propagated-inputs @@ -5877,14 +5894,14 @@ data.") (define-public r-metapod (package (name "r-metapod") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "metapod" version)) (sha256 (base32 - "1hbcwr6d8gyrf4azh0gi588xkrg6gz7gsb5hbvzqkhplbsp6shlv")))) + "1s8dfzpgbpxbn3jvx891gvw3jyn43nlxb73yv1vjn85brk9zbqpk")))) (properties `((upstream-name . "metapod"))) (build-system r-build-system) (propagated-inputs @@ -5906,14 +5923,14 @@ missing values and weighting where appropriate.") (define-public r-biocsingular (package (name "r-biocsingular") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 - "16gkwq8fb8jdchpnlzq2hz3i74a6pzbnc1bf93282h11mp7qr58l")))) + "0dkh6a23qymjcynppmpp3k1mzpfadv8dqyz410pxkqsxig4ldd4n")))) (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs @@ -5985,14 +6002,14 @@ maps.") (define-public r-savr (package (name "r-savr") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "savR" version)) (sha256 (base32 - "1ynp334hm76zf05j4f6vha6r16s5f2ncxx9yviq4rxidk9r723jq")))) + "0dwl94j5dm5ngn8lyyc4bd9ihd1nqincvq26najjn6lw0x55ciky")))) (properties `((upstream-name . "savR"))) (build-system r-build-system) (propagated-inputs @@ -6011,14 +6028,14 @@ Viewer (SAV) files, access data, and generate QC plots.") (define-public r-chipexoqual (package (name "r-chipexoqual") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPexoQual" version)) (sha256 (base32 - "0fbrf5s6pz115djm7xw95k1d0p7svi40aacbb3d52wmx5azwj424")))) + "1hh3mhfcngyx7cpzns8mjqviy8vfzrvxpv6nyizflpfmsr39mxfk")))) (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs @@ -6051,13 +6068,13 @@ sequencing data.") (define-public r-copynumber (package (name "r-copynumber") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "copynumber" version)) (sha256 (base32 - "03pvjzjrcsbjfw3855s3whfzin45vaipy7cahnj6fywdysvh8hps")))) + "143ifvjkjz0392drm82xmpj1f8b5pc2dyyxyc9dkqmay8lf1n534")))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) @@ -6074,14 +6091,14 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "0mgq814f6c2271d2lxg763bsnv3ma4ari5xa4x1rbksv8yvcjc4d")))) + "19ax431i97r49gh1232vf8mgmkvc6k26lnq44j3g10n6q01czswm")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -6174,14 +6191,14 @@ and regression inferences from RNA-sequencing data.") (define-public r-ebseq (package (name "r-ebseq") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBSeq" version)) (sha256 (base32 - "0h5v3vrb90zim80bdnr3aw58g3h7zjqa4l9i0jwx5j19ywf54fdz")))) + "1p8i04v5h6mbc8zqbf3rifbwwylzzc1fqrkhh0a0mbcgq2nv7i9m")))) (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs @@ -6198,13 +6215,13 @@ gene and isoform level using RNA-seq data") (define-public r-karyoploter (package (name "r-karyoploter") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "karyoploteR" version)) (sha256 (base32 - "11sgxz2xz685pgm8mf0hzm6aryx4fj5g3dlffjzpqxh3awfqa19p")))) + "0x3mld9q55r2fy452wxq5sjzmms10zmpkzs71c3w1fdli5hwszdq")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -6236,14 +6253,14 @@ coordinates.") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "0aw4b3p5z8ys7zlwy8s3bsqk03xwx42311yxr7q14w3f7sn3shzn")))) + "1bv28b1fgcazv6j0xw4nn6wljs37qnkyahqy7anrwissdpryhjfs")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -6266,14 +6283,14 @@ to install interface to SYMPHONY.") (define-public r-ihw (package (name "r-ihw") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IHW" version)) (sha256 (base32 - "0b393a8ayzbnrgkk562w1dj7avacpb3wc7yq7awiki24wi5g2lfw")))) + "0vgij5zyaw3fh7arkg4jy1mizsqzbkcsjl05mh3ng2bqh30kyqqx")))) (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs @@ -6298,14 +6315,14 @@ independent of the p-value under the null hypothesis.") (define-public r-icobra (package (name "r-icobra") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "190rkx3sivj68in36hhin5v535yd6fvlvm7l90w1bl38zpb7p6jn")))) + "0qg32g1rfvh6mx8wny1lrva9vc347288hzml7yb4rnrsx1hggkpa")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs @@ -6334,14 +6351,14 @@ interactive exploration of results.") (define-public r-residualmatrix (package (name "r-residualmatrix") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ResidualMatrix" version)) (sha256 (base32 - "0p7va19aw0j6anx7ck879kbi5cn7dy712h5ia94adr38ssismv1v")))) + "0xsn4fm34a7xpkgmx3a1j2xzdaxf2hyla1062wqn04kw0k9y29vg")))) (properties `((upstream-name . "ResidualMatrix"))) (build-system r-build-system) @@ -6365,14 +6382,14 @@ multiplication and calculation of row/column sums or means.") (define-public r-batchelor (package (name "r-batchelor") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "batchelor" version)) (sha256 (base32 - "1bkk69b5llkmvmpsnhymwjm2szmzypgszfsw8mak1b5ms5zf8lr0")))) + "0axkic11bwjbw8apwxx6p51s7jvlwhq7xi1bdknn54k86axq84dr")))) (properties `((upstream-name . "batchelor"))) (build-system r-build-system) (propagated-inputs @@ -6408,14 +6425,14 @@ the numbers of cells across batches.") (define-public r-mast (package (name "r-mast") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MAST" version)) (sha256 (base32 - "1gkpagam5rap36viyr3n4psa658x9vckrxap1h67jasiiyrcfz2d")))) + "14h6giny9lhzqjsx3h7gdhsm8wfwnvp5zsl4avrflip0jmsn45yy")))) (properties `((upstream-name . "MAST"))) (build-system r-build-system) (propagated-inputs @@ -6443,14 +6460,14 @@ single cell assay data.") (define-public r-monocle (package (name "r-monocle") - (version "2.20.0") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "monocle" version)) (sha256 (base32 - "05j1vc51f39xalggdq27y7218gkr3zq7fh7jhzsb4jj7fpn837ry")))) + "0wb2c1jf502lrfx3d0amb09fvhalrwxvpsp99jsab162v4hddg85")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -6600,14 +6617,14 @@ several functions from the R igraph package.") (define-public r-noiseq (package (name "r-noiseq") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "NOISeq" version)) (sha256 (base32 - "18d51dv2ygsm7kkwal341f1wrwrazyns0045j00vld367kic8jiz")))) + "0mmvzf8y4gm84hgjdpf86b1y37237wp5mc3x1g6sdiz9qi8l356v")))) (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs @@ -6627,14 +6644,14 @@ assumptions.") (define-public r-scdd (package (name "r-scdd") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDD" version)) (sha256 (base32 - "1dw9m3m99apmbs32461c6lnmy81n5hxbhz3p8jk419gajkh4v1ji")))) + "0gjdjkpkm9zc9hzzb6r2mknl4zyg7s2lgqppmzzhgcnvlmgvm5b5")))) (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs @@ -6665,14 +6682,14 @@ distributions.") (define-public r-scone (package (name "r-scone") - (version "1.16.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 - "0zw8g4mql7b02xqwhc1i0bnhm20c1q9xqc7yz84j98pqbi996vi5")))) + "1fqlwg195rzpwh35cj941vhmj2plzpn253skig6glr0z2sirr9r1")))) (build-system r-build-system) (propagated-inputs `(("r-aroma-light" ,r-aroma-light) @@ -6709,18 +6726,19 @@ high-throughput analyses.") (define-public r-geoquery (package (name "r-geoquery") - (version "2.60.0") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GEOquery" version)) (sha256 (base32 - "0jhkdbcd03d5n8vn3xkad6f21xjkawyxc9rdwcj8vwc8alx730am")))) + "0fkx4jh1s76l015vwikkryarlx6iihb1z935nzpdhah3rpqx3b3z")))) (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) + ("r-data-table" ,r-data-table) ("r-dplyr" ,r-dplyr) ("r-httr" ,r-httr) ("r-limma" ,r-limma) @@ -6742,14 +6760,14 @@ the bridge between GEO and BioConductor.") (define-public r-illuminaio (package (name "r-illuminaio") - (version "0.34.0") + (version "0.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "illuminaio" version)) (sha256 (base32 - "1sy0i3nbzsw4ymdxaiwpyx1vcg9yp3i8xfjcymqwhv95j3kyglv9")))) + "0icsp610am5vrd8x2h9c450phn4vl9c5wnzqmkix5hkqzrykk34m")))) (build-system r-build-system) (propagated-inputs `(("r-base64" ,r-base64))) @@ -6763,14 +6781,14 @@ files, including IDAT.") (define-public r-siggenes (package (name "r-siggenes") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "siggenes" version)) (sha256 (base32 - "0lva0f255fcpy625frvij4n14q7nw4jcx8n2hlkxid4mgkfqwlhf")))) + "1fymp5ci1nwkk5yfj7hli464xqvvlvzf2a5j0w3qkxly9hrymix9")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -6789,14 +6807,14 @@ Bayes Analyses of Microarrays} (EBAM).") (define-public r-bumphunter (package (name "r-bumphunter") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bumphunter" version)) (sha256 (base32 - "0wi38vwfi8qr10x4xifhylxx7vfc6fqvqs649iq7lf0y7islwq2v")))) + "0d5cz9xy7vhcaj5n3h4cfiv08sn7wn83458525pdwvdzzm449xgv")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -6823,14 +6841,14 @@ studies.") (define-public r-minfi (package (name "r-minfi") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 - "189lzppvrz6bw2kpppawgsfjyh2ahyy8bi9z8srpas67qf2r8jmj")))) + "0d5220nknwgi1020vhvf7408n5p80dmad66n85af5776qn84a6nx")))) (build-system r-build-system) (propagated-inputs `(("r-beanplot" ,r-beanplot) @@ -6874,14 +6892,14 @@ methylation arrays.") (define-public r-methylumi (package (name "r-methylumi") - (version "2.38.0") + (version "2.40.1") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 - "1941rc524ssx8gwhmwk40mgfrhddfs6hgldvs7bi22r29gm4y7qj")))) + "1lfcsv8k9c4ndfwlbdk3vd7fq58100bfijyxklna41zf8m8kkkka")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) @@ -6891,6 +6909,7 @@ methylation arrays.") ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19) ("r-genefilter" ,r-genefilter) ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-illuminaio" ,r-illuminaio) @@ -6920,14 +6939,14 @@ and Infinium HD arrays are also included.") (define-public r-lumi (package (name "r-lumi") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 - "0qjdxjdzfnnxcm07bf51v38388s5qf1i03l1sdb9jf3gxdh8yh02")))) + "0v33p66vn4alhx2il9wwdvc9sqvgasgj0s2gk85gjc76ad0017in")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -6959,14 +6978,14 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "035hrniycqadmkwg8rmzw8szv0amhy31390izy91rfrld31v2yy7")))) + "1bdnglznsfs1kdscqyjv595wiy09khcv9kxm4fmbnmksisqjz5qj")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs @@ -7020,14 +7039,14 @@ evaluation of DEG analysis methods.") (define-public r-ioniser (package (name "r-ioniser") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 - "0fknlwdfd49v09zspg0337b0zzc8hqza3563yrw51viw3g35d6q3")))) + "1hdg446z5s616aaalzz49if1wp9nmzm2mbyva82m1vz8i7ih9m4h")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs @@ -7117,13 +7136,13 @@ published results; and a routine for graphical display.") (define-public r-tradeseq (package (name "r-tradeseq") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tradeSeq" version)) (sha256 (base32 - "0fgmb309pvqf3chdhqgbd4lzhahcj5g71sica33nzn98qhipldx7")))) + "1s5anbb38gi5sfkxy19zpvkj8d0ij7m6cd0z4gmx4f5pf7pz0m3j")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -7132,10 +7151,10 @@ published results; and a routine for graphical display.") ("r-ggplot2" ,r-ggplot2) ("r-igraph" ,r-igraph) ("r-magrittr" ,r-magrittr) + ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-matrixstats" ,r-matrixstats) ("r-mgcv" ,r-mgcv) - ("r-monocle" ,r-monocle) ("r-pbapply" ,r-pbapply) ("r-princurve" ,r-princurve) ("r-rcolorbrewer" ,r-rcolorbrewer) @@ -7144,6 +7163,7 @@ published results; and a routine for graphical display.") ("r-slingshot" ,r-slingshot) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-tibble" ,r-tibble) + ("r-trajectoryutils" ,r-trajectoryutils) ("r-viridis" ,r-viridis))) (native-inputs `(("r-knitr" ,r-knitr))) @@ -7187,14 +7207,14 @@ peak definition in combination with known profile characteristics.") (define-public r-varianttools (package (name "r-varianttools") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 - "1gpzrln2clfrja8rzxhsis6bi1xqglh3h2lhvqlnrx4lqxhbkv9c")))) + "0079dsgav4q03c4i0dhggc88iifd828n73kjv3sahim9akafdshl")))) (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs @@ -7227,14 +7247,14 @@ gmapR.") (define-public r-heatplus (package (name "r-heatplus") - (version "3.0.0") + (version "3.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 - "0xwg3sxmihg3p6v3nxgrqy0nrqxi6razg3b3rjh2gcb2vv8gcqng")))) + "0yrnjrbfn8vjzvp2742lyxdqca4s18h73j44qxw7ib95x3p4lndf")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs @@ -7252,14 +7272,14 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.18.1") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "00dbgkiv9x7g2i0anzcxpycwqqqry0y7jl3ad93lhvi31qnqq1sm")))) + "15qi69kkgah7g25bymk9q1xf16hp1rd040fglg0svnydylg2d0ab")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs @@ -7281,14 +7301,14 @@ sets of GO terms, gene products and gene clusters.") (define-public r-anota (package (name "r-anota") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 - "039bmcv5l44gszb6xapbihp3mfqdaaa8mfc05y702p78i7x93g5y")))) + "0agvcpb3lr9v55h53ywf662gpxayivxacv8dcm526cc8i8hdqa9f")))) (build-system r-build-system) (propagated-inputs `(("r-multtest" ,r-multtest) @@ -7312,14 +7332,14 @@ the data set is suitable for such analysis.") (define-public r-sigpathway (package (name "r-sigpathway") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 - "1xz5nbw5dzyah8az7mpwj8m27fsvpi2jjhfg3n27dsv8rvdncqi8")))) + "1c46m1gbgiygcj8m65h8iwzk3fkp6nynd6rk1f5qdh7kw5ap28f9")))) (properties `((upstream-name . "sigPathway"))) (build-system r-build-system) (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") @@ -7334,17 +7354,19 @@ phenotype of interest.") (define-public r-fcscan (package (name "r-fcscan") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fcScan" version)) (sha256 - (base32 "10fcz741dr3wbb9f63qywlrays4cnvfnsm6yw4bmkrwk6ccijg8h")))) + (base32 "0b161ayq4m9xxfs0lgw632lgygzabz8gjl0n75050pa7qaazknvd")))) (properties `((upstream-name . "fcScan"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) + `(("r-doparallel" ,r-doparallel) + ("r-foreach" ,r-foreach) + ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-plyr" ,r-plyr) ("r-rtracklayer" ,r-rtracklayer) @@ -7365,14 +7387,14 @@ presence of additional sites within the allowed window size.") (define-public r-fgsea (package (name "r-fgsea") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 - "1mhdgy46nxgv7v54bk9bqfy0vgjzl1law7zy718swdd762xn6g9d")))) + "10flcdm4b1kxnsvhl4k6mwkzb1vbai33k291j8nsrhj2cl5l8gm9")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) @@ -7397,14 +7419,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.18.2") + (version "3.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "0kp6j42mpxrpd02cjrzqmrx3rvvpi90xiy4gc5km6ny3vxbhlaqw")))) + "0hj5hn54g8a3gj4q9200bffcy9m1mvkiwbg60ysv1hxxbpi57kmv")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs @@ -7432,17 +7454,17 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.12.2") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "194sfmcnjfi3fvvfpljg1f80f44vvvxiij336b8z1dgzki6bqa3r")))) + "0nsx96mkcg0hhg3x8jndzq3xvq9bq7m4yf1b3ry73b17ladx81ch")))) (build-system r-build-system) (propagated-inputs - `(("r-cowplot" ,r-cowplot) + `(("r-aplot" ,r-aplot) ("r-dose" ,r-dose) ("r-ggplot2" ,r-ggplot2) ("r-ggraph" ,r-ggraph) @@ -7455,7 +7477,8 @@ data.") ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-reshape2" ,r-reshape2) ("r-scatterpie" ,r-scatterpie) - ("r-shadowtext" ,r-shadowtext))) + ("r-shadowtext" ,r-shadowtext) + ("r-yulab-utils" ,r-yulab-utils))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/GuangchuangYu/enrichplot") @@ -7469,14 +7492,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.0.5") + (version "4.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "1dccrl2ffhgmv3iqlmpln7z86ahpf0j9ma194fnknsgi3cd9rhrl")))) + "18y7482sw0awlhazikq13r2r0zid9ksk942rma87m448y1cq2fi5")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -7506,13 +7529,13 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-clusterexperiment (package (name "r-clusterexperiment") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterExperiment" version)) (sha256 (base32 - "1fhmayciwn1m124b4dcs3gzbghgk9f7a7qmjnvvxc958cywcwkx5")))) + "0riray1f841d5fx6mbcki5xmqz21kg5q5l0qz4pkgg9c1d9f7mbc")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) @@ -7552,14 +7575,14 @@ expression data sets.") (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "0ipzv7wdvfqhdyjiak956qq201igsdxm6dr6rh3dj6cssgsrnrpb")))) + "1nzy04fqwzb0ywiafgx3m3i2n1b0g4pcg8mlgh8yz5d3mmna4kag")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs @@ -7594,14 +7617,14 @@ data in R and Bioconductor containers.") (define-public r-annaffy (package (name "r-annaffy") - (version "1.64.2") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annaffy" version)) (sha256 (base32 - "03y633vgxprd2abhanj4sanmb4ymz7az5aiasxn6wjzawiqjdcb1")))) + "0crj37v571005brdd0ypfx2a7d1f829xxj2hahp2gy8aj9xm4s8l")))) (build-system r-build-system) (arguments `(#:phases @@ -7630,14 +7653,14 @@ It allows searching of biological metadata using various criteria.") (define-public r-a4core (package (name "r-a4core") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Core" version)) (sha256 (base32 - "00fi753nsayv0xspavw8r9ni1sim8ng33hp3d3kj2b8ihygd1s10")))) + "074aa52y6c70417lxwrclk613gbs7zv3326g9ndbbzzs5pmnh1y0")))) (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs @@ -7655,14 +7678,14 @@ arrays.") (define-public r-a4classif (package (name "r-a4classif") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Classif" version)) (sha256 (base32 - "1lz85bys5dp5d1ir9c9c4wy85wkk62s14niyzzxaqrxpsji2p2iw")))) + "0q50d41n7drj5c9x6njyvzr6bj7glmkp1vpyz6cpj97j2v9nikwb")))) (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs @@ -7685,14 +7708,14 @@ Affymetrix arrays.") (define-public r-a4preproc (package (name "r-a4preproc") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Preproc" version)) (sha256 (base32 - "1jibm2f5glzsrvl64hxc5sf59d4w6ry0f663p619hfr44mi1mpri")))) + "1qzr54w1qys1ppd71i5b57503dijfnnbn516a2mfk5l9l7wr728d")))) (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs @@ -7710,14 +7733,14 @@ is used for preprocessing the arrays.") (define-public r-a4reporting (package (name "r-a4reporting") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Reporting" version)) (sha256 (base32 - "09jjfby5znmg2fdkhpbinx2v21zrfa44qq7cylcn9ipffqx3pk86")))) + "1vyah71gm4ngsgy0y10cdxa9b1g810gqa5pbvb3krh5i6h35smwr")))) (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs @@ -7734,14 +7757,14 @@ provides reporting features.") (define-public r-a4base (package (name "r-a4base") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Base" version)) (sha256 (base32 - "101w4i0w8n7qhki22qr8l8wk8w6zalzmcywqm2g4238qv7xbnr8p")))) + "0rddxnflvbc6z4sj2h8js8yfh0zhrrwj8fk00wicaqp4rkr5yaxy")))) (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs @@ -7765,14 +7788,14 @@ Affymetrix arrays.") (define-public r-a4 (package (name "r-a4") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4" version)) (sha256 (base32 - "0bwn185admy5k99fkd2dhhvy7x1f75r0mqn5k24dbbg0paw6nnr8")))) + "0mkgim93441zxhn4wmbin9ydl94srsawis0xwx479l0byj88n07m")))) (build-system r-build-system) (propagated-inputs `(("r-a4base" ,r-a4base) @@ -7790,14 +7813,14 @@ Affymetrix arrays.") (define-public r-abseqr (package (name "r-abseqr") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "abseqR" version)) (sha256 (base32 - "1xvk84gd1lfq1icrfwwd6y79zywrisfnc3knprigzzax31aks32c")))) + "1v9g71x689ly107c0qmc5iv8qk63nn6lp7yd03jf7hlcafmvqsvz")))) (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs @@ -7838,14 +7861,14 @@ further downstream analysis on its output.") (define-public r-bacon (package (name "r-bacon") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bacon" version)) (sha256 (base32 - "1yp0675n1g8rxdjdd7w8al5c9jq96h0kfm8218mc50z0p2fasgbj")))) + "13dhma34j9ggryainn4x6qvd3hphpxks5gf0mysia00r9hhpwwlc")))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) @@ -7865,14 +7888,14 @@ fitting a three-component normal mixture on z-scores.") (define-public r-rgadem (package (name "r-rgadem") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGADEM" version)) (sha256 (base32 - "05drbhjqn5kik6k4h03vr3d2b6pv5rm65lsnkyx4caxxcdii4jzm")))) + "1v8xgqqv7m2kyc38x9ppwsv87ivll5ppd6z76zcxj5yspkkrqw3v")))) (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs @@ -7923,12 +7946,12 @@ distributions, modules and filter motifs.") (define-public r-motifdb (package (name "r-motifdb") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotifDb" version)) (sha256 - (base32 "04cmgg5mw1cqbg95zyfc2imykmdxyff16w26rq97xghcxwiq2b3z")))) + (base32 "0a2zg26zzk7bj5c33mbwl8dx9lh1hns8q8kwp09rbfjdichv7425")))) (properties `((upstream-name . "MotifDb"))) (build-system r-build-system) (propagated-inputs @@ -7950,12 +7973,12 @@ frequency matrices from nine public sources, for multiple organisms.") (define-public r-motifbreakr (package (name "r-motifbreakr") - (version "2.6.1") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifbreakR" version)) (sha256 - (base32 "1n6v8a7c27aswmbrlcwcpghf27aplkc6nn923imglc3c0sh2lkrz")))) + (base32 "0lrgy64sv2ma6kylp4lsbwkg6ci1kn6qkk0cvzw3m4k3bgia1npj")))) (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs @@ -8001,14 +8024,14 @@ Bioconductor.") (define-public r-motifstack (package (name "r-motifstack") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 - "0yn348kmw7v46iym913ncx4yh5nxzmba8bdys52s12ldgjja53gp")))) + "1ck6bbnrab8mbf70alfdsrcv6lq0fkvcy3klhcwyxxir7r9sgbaz")))) (properties `((upstream-name . "motifStack"))) (build-system r-build-system) (propagated-inputs @@ -8032,14 +8055,14 @@ type and symbol colors.") (define-public r-genomicscores (package (name "r-genomicscores") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 - "1b8982fj0r7igj749wljsdfn3c985w8n3d5gbhr5rw73llfb8x6w")))) + "18fzi2qi95851ci7qrzwpb7v6fhwp6xi1d1vk11xbygpbvql5mls")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs @@ -8069,14 +8092,14 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "168g3xkhjzrfjpa1ynifdyfhsxx3rpyrbybsarlzr9kslw1cdkxl")))) + "0i1i3bfkp1xsjdl1nd56mlh66qz3aasd1hp09d4i31njz2f9znwn")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs @@ -8116,14 +8139,14 @@ footprints.") (define-public r-gofuncr (package (name "r-gofuncr") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOfuncR" version)) (sha256 (base32 - "0lp2gmjlsk1yqxim5pi26i27iijw11lrcxmji7ynlag359yfnynd")))) + "08n1d03i4l2dl47axmrziiypi83yffndf0ww1b32skyjm2r0x127")))) (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs @@ -8165,14 +8188,14 @@ annotations and ontologies.") (define-public r-abaenrichment (package (name "r-abaenrichment") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABAEnrichment" version)) (sha256 (base32 - "15v5n6d3mnj9d86swkh9agfvrsd065dldaywm1adwmkhhk525wmd")))) + "1sp3f72rzlr822dxx42bswynrwwfx6f520hdhfdikqp13p2y4044")))) (properties `((upstream-name . "ABAEnrichment"))) (build-system r-build-system) (propagated-inputs @@ -8222,14 +8245,14 @@ different identifieres using the Biocore Data Team data-packages (e.g. (define-public r-annotationtools (package (name "r-annotationtools") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 - "18dd8saqx17fplvv5sbfz4p9fy7ksy3n9348rd3qlczihcrh9i3w")))) + "0grdswbf8nj0qwl0n5pqsir9242dry85j6m688j81gwwjgmzidvh")))) (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) @@ -8247,14 +8270,14 @@ text files).") (define-public r-allelicimbalance (package (name "r-allelicimbalance") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AllelicImbalance" version)) (sha256 (base32 - "1mn6975npncmfjlpjs3s2pgsrm32xgvnyl2vh1922l6vra97dkrc")))) + "1s6arjd0nxgxyqy7vhqcb78k0ss7vwrhv41pm346hs1nyr5dkzaq")))) (properties `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) @@ -8290,14 +8313,14 @@ investigation using RNA-seq data.") (define-public r-aucell (package (name "r-aucell") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "0qdac3qalcki20r90k40cc8d0lfywzn9pffg9d719yvs7nrsfdjr")))) + "1lclf8hkhrm6g5fp8yhvjxnwgf8p0j9ffxsmcybz4rjvmwkiz5dp")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs @@ -8329,14 +8352,14 @@ needed.") (define-public r-ebimage (package (name "r-ebimage") - (version "4.34.0") + (version "4.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 - "1z3cxxg593d66nczz5hh2hdj1d87wc0lxrzc5sn6bp43n351q8h3")))) + "030vpn55ppfqq4408c4db4w40d17x1yq6zajb11p2glikvm1q619")))) (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs @@ -8368,14 +8391,14 @@ visualization with image data.") (define-public r-yamss (package (name "r-yamss") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 - "1al615x778h17jqiyhiyf6djaq9iygs1hlbrna6y4xc0f2kvgxld")))) + "141hbryifm6na5shjyrbjwwksqnl75kqp1m2zl03l9sjqm0kapab")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -8402,14 +8425,14 @@ analysis.") (define-public r-gtrellis (package (name "r-gtrellis") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 - "0l5271cpzjlm4m0v6xcdg2vxlbhn53x1fd59ynb9jwll93av5h1f")))) + "0q2lyb8p1xhqqhw4q1br4r8mwq06mjws8iwbbilkngvs3brbmrzl")))) (build-system r-build-system) (propagated-inputs `(("r-circlize" ,r-circlize) @@ -8431,14 +8454,14 @@ genomic categories and to add self-defined graphics in the plot.") (define-public r-somaticsignatures (package (name "r-somaticsignatures") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 - "0jr11c9hz7m49xc8pi6xrr5fhbv68vafvqpzhr0pmm51vvr1vfs9")))) + "1dxzfkvljnydv7kfybfa52dwcbkkci2r8gjspjf90k2bxf10phql")))) (properties `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) @@ -8470,14 +8493,14 @@ decomposition algorithms.") (define-public r-yapsa (package (name "r-yapsa") - (version "1.18.0") + (version "1.19.0") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 - "1xfkgjlm0rxz82qcaqzx95cwirxifd9dsswjg3zcqmz03v7a0gz2")))) + "0fgcbskz96p5815nywsnqv2gzn7g93m438hpd5rpg85srg4wrpdj")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs @@ -8519,14 +8542,14 @@ provided.") (define-public r-gcrma (package (name "r-gcrma") - (version "2.64.0") + (version "2.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 - "1z4abw9s2hs3csnx25nli7fpvb3rh3l0swzl0wfqp087fcs78pxi")))) + "0h7dl4if6skbcqdjdzqyghyswhwpx7xvb54lffz4wdaxpabp3001")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -8605,14 +8628,14 @@ chips with the MAQC reference datasets.") (define-public r-quantro (package (name "r-quantro") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 - "1fkma2ic448h2lrlza8ipg65gpfsz4fhlxcnjpmzhhmzp2xi2p4a")))) + "1r2wbsndc0ji22ap27gbr1wy8icj3cjxwqlz1x0gvxkaj69mwsfq")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -8638,14 +8661,14 @@ groups.") (define-public r-yarn (package (name "r-yarn") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 - "1x07l255x52z6cgdc2j8285shqszhr034xm5686rp6d35vah55ji")))) + "0nk4qzrwjiv8q39lgil9x25bm3gpzrnhd37d7754kpxhs2fsmw9d")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -8675,14 +8698,14 @@ large RNA-seq experiments.") (define-public r-roar (package (name "r-roar") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 - "0vp0n90rvjm8rzwkbrxa3fasb9val56bz2srz72xwsl3jzb5yk6w")))) + "0hqh4vsnxl2sn1bf6s6wxl2nskb40rhvrysdvb6dr60zkih3g347")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -8743,14 +8766,14 @@ genes.") (define-public r-massspecwavelet (package (name "r-massspecwavelet") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 - "1cs32sig1yvqn9xs0cvhfpmkh2lbllx7aab80sz58x03wnx8v60z")))) + "1icqyxkx5a9y3wahkxpxngw85c7l4hih1ym9nwwn9qy93pnw1zi4")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) @@ -8767,14 +8790,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "3.14.1") + (version "3.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "1g8k90p0sbcb3rdrbldj5bcjp2piy5ldni4jplyr78vjpmrmvqk7")))) + "0m6w68ndf2a4k148pbb0bbbgq57akzqgi9nf7k6ngkk22j3m7m95")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -8784,6 +8807,7 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") ("r-lattice" ,r-lattice) ("r-massspecwavelet" ,r-massspecwavelet) ("r-mscoreutils" ,r-mscoreutils) + ("r-msfeatures" ,r-msfeatures) ("r-msnbase" ,r-msnbase) ("r-mzr" ,r-mzr) ("r-plyr" ,r-plyr) @@ -8807,14 +8831,14 @@ data for high-throughput, untargeted analyte profiling.") (define-public r-wrench (package (name "r-wrench") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 - "0yssmqayaryrc0asjjqxdipqdfg309llrzldx38jrfgdsza6bvs0")))) + "1vzv7sswijgb8nq58yrc19wlw2nnpjvans86fqqzs4p8wvq8j06n")))) (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs @@ -8833,14 +8857,14 @@ that arising from 16s metagenomic surveys.") (define-public r-wiggleplotr (package (name "r-wiggleplotr") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 - "13f3g6fcc29k0g21mhnypm3nc6qqjw867vamvfkdzynspsfb32ga")))) + "01y1rbmxjza7qx3q33k0r241if69hzkx9plgmj59wyji22lm7syi")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -8867,14 +8891,14 @@ visualization of exonic read coverage.") (define-public r-widgettools (package (name "r-widgettools") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 - "186xgpgyfyi4angxhz6558lfpzvvszzlpyfr8xnbccs3gshk3db2")))) + "0jajfh78116wjfwbmzfvcbxswai4jj9ypzmfhs5j5iypaf8zff8j")))) (properties `((upstream-name . "widgetTools"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/widgetTools/") @@ -8888,14 +8912,14 @@ widgets in R.") (define-public r-webbioc (package (name "r-webbioc") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 - "1mpdw477j78s2nvlf2lzm6mdjcpamyyazjn060h9q3apawn6zajx")))) + "1r3rjvfhqbbzdhlslnc86kr2iip3xgvr81zpvcr8xv9mysgrln17")))) (build-system r-build-system) (inputs `(("netpbm" ,netpbm) @@ -8921,14 +8945,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.") (define-public r-zinbwave (package (name "r-zinbwave") - (version "1.14.2") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zinbwave" version)) (sha256 (base32 - "1y8krazz2qdn0wn8ijjs2gn5dl5l960v6bijbkvh0r8066l7viky")))) + "05w95bnq63a339d8x4932k81ycqf825s3qwn98vr52v5g2hv46fq")))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) @@ -8954,14 +8978,14 @@ the data.") (define-public r-zfpkm (package (name "r-zfpkm") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 - "1k7xaxr2gn26y8bps5l32g2axfhdn07nbk4q3qcx32d5jm75qkx2")))) + "0fk05vrmyyrhmkwi06lsi553mlpqj3fgwhk1kygz83iqv5z2vfw9")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs @@ -8983,18 +9007,22 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (define-public r-rbowtie2 (package (name "r-rbowtie2") - (version "1.14.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 - "0r5yqjal48xlcv5cidi7p3zwygvsllmv2zzkwkc9kfq083l2i4ih")))) + "0xpvrx2ak9x913sym4l46ycwbnmpcdwb3bf3dfd2gsp0krv8vh1x")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) + (propagated-inputs + `(("r-magrittr" ,r-magrittr) + ("r-rsamtools" ,r-rsamtools))) (inputs - `(("zlib" ,zlib))) + `(("samtools" ,samtools) + ("zlib" ,zlib))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/Rbowtie2/") @@ -9008,14 +9036,14 @@ rapid adapter trimming, identification, and read merging.") (define-public r-progeny (package (name "r-progeny") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "progeny" version)) (sha256 (base32 - "10vpjvl4wps857xiy8rpzr82jzdfbc5rgwh3ir3my26lfws4hfz8")))) + "0zhr5i5v87akzqjb6wid67nhg2icrw6w0awdy87x848c6c1i6j9y")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -9038,14 +9066,14 @@ expression\".") (define-public r-arrmnormalization (package (name "r-arrmnormalization") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 - "0ni3vblcadhwxaq1pf1n9jn66cp3bqch68ww4c8zh19zagil2y7r")))) + "1ryqr3mpakjml0jhbk28k2z511sdl87wxdczxq1rwx98s0pc9mnh")))) (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) @@ -9061,14 +9089,14 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "0ymg4hmabk233qgassld62achjylm12rnidxbakfkx4dvvlbhxxv")))) + "11qayqmgv274hc4h1v222sma07wkxjm8002fl6w3yvi225zq1qc1")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs @@ -9094,14 +9122,14 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "1haj25c4cmmjjvh181b41a9pvkh92f7k2w4ljn17iqg31vm45za1")))) + "0w6r2clk8wdnnnjmq3cspmxiq1c8vwprd66xmdrhcqzbjkpkdw2b")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -9124,18 +9152,16 @@ Gaussian distributions.") (define-public r-rbowtie (package (name "r-rbowtie") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie" version)) (sha256 (base32 - "0mfikbrs28q7r3lnsq0jma5x6nkrnm3q46242jh35w9c969jk5yy")))) + "0ardmryx6ac7v6n900a1klrrldvbmh7bxvy8ldz8rwid19h29ikr")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) - (inputs - `(("zlib" ,zlib))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/Rbowtie/") @@ -9149,14 +9175,14 @@ alignment tool.") (define-public r-sgseq (package (name "r-sgseq") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SGSeq" version)) (sha256 (base32 - "0i1yaw8h8gibakvaf1xd6nnjx2bsb2s9c0q74rbq9lm7haihivp6")))) + "15l0r6svs27k82dd472is26shwayz6rs5ylg5gpf3mldr7sa5kja")))) (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) (propagated-inputs @@ -9192,14 +9218,14 @@ interpretation.") (define-public r-rhisat2 (package (name "r-rhisat2") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 - "1hqahh5h22mj2crqp6r9xnm111xmfgk39c100rcaziqrpdy5npk8")))) + "092rws9vjxgm2jpkbp6ign47zmillyyidnc7ylcbn4zr9j5lwv0y")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (arguments @@ -9232,21 +9258,20 @@ index.") (define-public r-quasr (package (name "r-quasr") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 - "1635ff11ahzjrh3cdcxrq5bgd100n444k7mc0maz0jx21vj8qqb1")))) + "0d292xgaq8d3cdpa9anabda03lis46xc29iw9c5k5i3sj7dcr4g5")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) ("r-biocparallel" ,r-biocparallel) ("r-biostrings" ,r-biostrings) ("r-bsgenome" ,r-bsgenome) @@ -9275,14 +9300,14 @@ quantification of genomic regions of interest.") (define-public r-rqc (package (name "r-rqc") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 - "02hwj2vd003x0zf273ndnwh7kxy6wc3sz14d3kryp2w2aqjj826f")))) + "0hcxkrfja0gmd8r2llijdvaw2xiiplk037305inimz0qna6w2071")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs @@ -9318,14 +9343,14 @@ graphics.") (define-public r-birewire (package (name "r-birewire") - (version "3.24.0") + (version "3.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 - "0p6mr67mkw54490sv4dvkyh8l0xkpjfbqy532vi8l41i40qg3gry")))) + "0ki4rcwjgbixzy5q9s30ajx5zhpl18q50znrb60fchvl4hj9h93w")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs @@ -9376,14 +9401,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") (define-public r-multidataset (package (name "r-multidataset") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 - "1hyk40xgmy50rqxwdvc64d3pgz5vsg8vmlj5cp5m0n5m0adxcdfj")))) + "17asldnxqvp3sijx7nbi2lbbgnq4iq8z72qlg9080sm5lga1yy1s")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs @@ -9413,14 +9438,14 @@ packages.") (define-public r-ropls (package (name "r-ropls") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "1j99kdywyljqzdcns5ysh590w4w8iiwzpddpfk5c8d4whax7vk5b")))) + "0mz5lrdsihx66sgx9klnvpxvw1mjjcbijcsdbgxwaimzl9k1kr05")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -9451,14 +9476,14 @@ coefficients).") (define-public r-biosigner (package (name "r-biosigner") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 - "159fbkymn92li7dinsm56nsacjp8wnhsljv7airgs9m82p8wd5sl")))) + "189018qahyw33dmg73wa7k4rp8nzrx6ai8f2dr6vhbpcdc1gnm0z")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -9484,14 +9509,14 @@ datasets.") (define-public r-annotatr (package (name "r-annotatr") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 - "1ls1qdfppcxysggi3bghrnspb5a3s40pm2mj4x0whc7c40cf90mg")))) + "1ha2wn56cdab4p3wdwv4xlqjsgl7sd8phbx71qbclrbdwpq2mi7i")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -9525,14 +9550,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.6.4") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "043m4512q73x6q529hqfgrap0fq5anvny4va085nafia06b805pi")))) + "09kd7vl2z9k82ppfzy679hs7d00c60z3w3n6a8wq4z3k3f4glc3s")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -9551,14 +9576,14 @@ and to both short and long sequence reads.") (define-public r-flowutils (package (name "r-flowutils") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowUtils" version)) (sha256 (base32 - "1sdwgyvrsz0pp60zdfrcgb7bs8s87j7257p8ck813ydizc324x9w")))) + "0rgybkzbn8c3kpbz0ddghp1np0gka0cgiqvkk5jbnhlgf4s07161")))) (properties `((upstream-name . "flowUtils"))) (build-system r-build-system) (propagated-inputs @@ -9577,14 +9602,14 @@ and to both short and long sequence reads.") (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 - "163nr50nyvwrsajmm0cgxp70pqk61mgw0k7ams694hcb42162j8b")))) + "13z43qbk9z7mvy8v8k185m6n020i6ahb18pm4q88rs75qlklzdkr")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) @@ -9602,14 +9627,14 @@ cluster count and membership by stability evidence in unsupervised analysis.") (define-public r-cytolib (package (name "r-cytolib") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "0wl7zqwv0i38dfzqfsz40n3mcbxi38ffn1rbd5pm9s7hq16zr4nv")))) + "01r5dfjil1i526kb5gj9c8x9agi90x0bh7lzykbpn0g6s2hznbzi")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (native-inputs @@ -9631,14 +9656,14 @@ interact with gated cytometry data.") (define-public r-flowcore (package (name "r-flowcore") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 - "13xpbkxi53rxmhvpdiy6bydmhicmxd2gi96d9c1qx4lkss2f14nc")))) + "0zbd2hrdbb6r0np6nd3ab8nlcf9l57vcwnnhbqkbas8y0c2i2mwp")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs @@ -9663,14 +9688,14 @@ with flow cytometry data.") (define-public r-flowmeans (package (name "r-flowmeans") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowMeans" version)) (sha256 (base32 - "1awskkq48qhv4v9glxgfqi0kgwqd62fbj641k4vvxfcwsf2c7bfg")))) + "0iy8hvi0inj1ylhdx6q4mya9k55iazprz6fdrnq1mxb2iyndzsl6")))) (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs @@ -9689,14 +9714,14 @@ change point detection.") (define-public r-ncdfflow (package (name "r-ncdfflow") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ncdfFlow" version)) (sha256 (base32 - "1lm88qnfv6rnnr7wmgbvwyj272imjjjn7h3agxqqzsbmn8vyrnf0")))) + "1c6wb2x24ydqp5nxrx6bhj6f13x9djfy9awkc7zn63xkag7mvvar")))) (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) (propagated-inputs @@ -9720,14 +9745,14 @@ manipulation of flow cytometry data.") (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "0jd6m84m4znnpix4bcgdby7mnflsn206f5x2vw9n8rxnwzx77wpg")))) + "17dnmsa92gc2za36c3klgd7rklqlxrhkzs5ksnrc1am6a4knc0p1")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs @@ -9757,14 +9782,14 @@ statistics to the plot.") (define-public r-flowviz (package (name "r-flowviz") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowViz" version)) (sha256 (base32 - "17x04xwyw2pp5zkhgvrmxkb8cbrv9wql6xhjsfpq0n6yd9dxqc1v")))) + "039sh7qn25gp2b34khs8dyrdpxyapsjlprrvxlz8f7dl8gmggl04")))) (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs @@ -9788,14 +9813,14 @@ statistics to the plot.") (define-public r-flowclust (package (name "r-flowclust") - (version "3.30.0") + (version "3.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowClust" version)) (sha256 (base32 - "03xsmprrkxwkaksjlaxwp54mqfb3zlg6dbqhp87w78fwscisv76b")))) + "0ch7mkq40qcnxwgzy51vjdlwyzx4bvp03vpdm6dwjc6qy8a6qfzi")))) (properties `((upstream-name . "flowClust"))) (build-system r-build-system) (arguments @@ -9811,6 +9836,7 @@ statistics to the plot.") ("r-flowviz" ,r-flowviz) ("r-graph" ,r-graph) ("r-mnormt" ,r-mnormt))) + #; (inputs `(("gsl" ,gsl))) (native-inputs @@ -9828,14 +9854,14 @@ model with Box-Cox transformation.") (define-public r-rprotobuflib (package (name "r-rprotobuflib") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RProtoBufLib" version)) (sha256 (base32 - "1hyds97ay4mn7nl830yh9v8mlasgsljsx5wsrhz2zsmbbyx6wbnb")))) + "04qlhbhdchpr35rdc6jc3y8fy6znnfrdlsb8am04agbrvpjgrx10")))) (properties `((upstream-name . "RProtoBufLib"))) (build-system r-build-system) (arguments @@ -9857,14 +9883,14 @@ for other R packages to compile and link against.") (define-public r-flowworkspace (package (name "r-flowworkspace") - (version "4.4.0") + (version "4.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 - "1a9qb2dcvwgb3z0vdbbzn1rzy77d3da72kirs272344hdx9b2cx9")))) + "11ni7kgk9s1fz3lvg85s6r7x2fhk4m7cdpilji05ya12jsyr3fig")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (propagated-inputs @@ -9911,14 +9937,14 @@ matches the flowJo analysis.") (define-public r-flowstats (package (name "r-flowstats") - (version "4.4.0") + (version "4.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 - "1yr5m7qmhmm52c70z3d0zy4zgf0hja7r2ig9yljv5w86bzm962x6")))) + "0jjfq66m4lbpkynwxaparkd05znhp3jl9ccj37gyghly294x3rm9")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs @@ -9947,14 +9973,14 @@ package.") (define-public r-opencyto (package (name "r-opencyto") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 - "1par1d5pk1rjg15q7i5z5wqma7xg6fycb826a823wk8wr52a885x")))) + "11svr1lk383pkm4npwrnf3h37b3drjsmcwcgdbb45x8k2k95z2fm")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs @@ -9991,14 +10017,14 @@ sequential way to mimic the manual gating strategy.") (define-public r-cytoml (package (name "r-cytoml") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 - "0ixy7mmnipk8wy61wz6qy7jfbc5zhs6p5iqaii8hdprjnb841ri7")))) + "16rgsc2dz5b8lm3ma8nh9wiknrdnvfjcsij7809rmcfs0gn1arcz")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (inputs @@ -10044,14 +10070,14 @@ standard to exchange gated cytometry data with other software platforms.") (define-public r-flowsom (package (name "r-flowsom") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 - "18h7p7g3w9imyd1c93jllgp4kd74z96cs85wcqfhmd26nx18hl82")))) + "062xrv8li2z849qa8mv5dhafqli6ziz099ikjfvi7v2fr7174p8f")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs @@ -10087,14 +10113,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.16.3") + (version "6.17.26") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "1x6dbw4q6p9vngm256fr96r9fjxk5nik5ivkhbl5a9zqyq8wagpa")))) + "10ir4876sjmw2mw0cjvshwy3qyhsyz6g1ihyr3dycgzya0jcxw1x")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs @@ -10133,14 +10159,14 @@ delete entire rows with missing data.") (define-public r-depecher (package ;Source/Weave error (name "r-depecher") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 - "04vxc43p3kpsx0vksk2nwmy9p56h35z2mc8j9p2wm29zaz1y8j3p")))) + "1500jivij7zdycdd0i0b7mgp44w4z0hqnpzqbq8nhvzzdigic8x9")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs @@ -10179,14 +10205,14 @@ data, to only emphasize the data that actually matters.") (define-public r-rcistarget (package (name "r-rcistarget") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 - "1yh0l11vnslgr6zsbpgc8mc4aa32zy34f5yrz98hkcdl53iw5y7f")))) + "1qarr7xd71kz1haccj65x7sc7pc4v6xpqcfa3rkyp2bk240gigi7")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs @@ -10221,14 +10247,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-chicago (package (name "r-chicago") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Chicago" version)) (sha256 (base32 - "0dkwy6pfvzd7g4qmhjl24ypn92l78w1zy0ajhcxgg39f7zsq883x")))) + "0nz9v37p7zl8yw3ykdbsb3izcwgx349wvrhwfyyn9h3jxjfafngn")))) (properties `((upstream-name . "Chicago"))) (build-system r-build-system) (propagated-inputs @@ -10247,14 +10273,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-cicero (package (name "r-cicero") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "1y34cm52bv1v2hr7sz8zjzxwd4wng7v75avz5wx45l0ld54z9l10")))) + "1fc69nkm2cwpr6gkfmra2ph0lrmw486chswp4pn8i70ia43fzdm7")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -10314,14 +10340,14 @@ accessibility data.") (define-public r-circrnaprofiler (package (name "r-circrnaprofiler") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "circRNAprofiler" version)) (sha256 (base32 - "1hif40vfg2lkbyf6abbkxbdm3b1biw6gxnh6ca2sydvi3y5l2ys2")))) + "0l83r9idhrha1m21vpnw917m5dlldji49zvx4d25m5g3ia1pkhpf")))) (properties `((upstream-name . "circRNAprofiler"))) (build-system r-build-system) @@ -10449,14 +10475,14 @@ cisTopics and explore the nature and regulatory proteins driving them.") (define-public r-genie3 (package (name "r-genie3") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 - "1v54dzcz654wfm3npbp8gb55v49im0fm547cz3hvsidq4zhi3l1b")))) + "0ms769267pimrx3xwwkgjy03qilkxxs7xwhzfca01f65i4n3l6fw")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs @@ -10474,17 +10500,17 @@ regulatory networks from expression data.") (define-public r-roc (package (name "r-roc") - (version "1.68.1") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 - "1rmsrvn6hrg9ay7xfb05mfkxknnig78p3kbk9ghsd11lhx2fjm3s")))) + "1mgxpv5p6gnv04wzkcryrg5as5xrxvlqlkkcbv0k1bx9y6ykijy9")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) - (propagated-inputs + (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://www.bioconductor.org/packages/ROC/") (synopsis "Utilities for ROC curves") @@ -10522,14 +10548,14 @@ data.") (define-public r-watermelon (package (name "r-watermelon") - (version "1.36.0") + (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 - "1qar8z0nf33bqr488swig0bfq8lnvcdjcxvw3q3b0hkkvybn27zw")))) + "1kzkg3cnm5pcs6blpw1qn7na6z3kar93v67680wsxa6qxxdiggk3")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs @@ -10542,6 +10568,8 @@ data.") ("r-matrixstats" ,r-matrixstats) ("r-methylumi" ,r-methylumi) ("r-roc" ,r-roc))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/wateRmelon/") (synopsis "Illumina 450 methylation array normalization and metrics") (description @@ -10559,14 +10587,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.28.1") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "1w3z718q3bhh8bp71va9pbcd62pwbvgjw33ffg960jya40xssvc7")) + "147i33sb65n3cl3ibmjzgfm7i4ljy640k18mzknvc18v1906j9vp")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. @@ -10617,14 +10645,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-bigmelon (package (name "r-bigmelon") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 - "061f0hc4m4nvdr6298pg3inpx1z2bpsm9nlxqs3v7n58q15xyzri")))) + "0ksbmybi8wsg515b4k9ij1xqqk9i90pyap2wq5w3c49qgc0pqali")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs @@ -10632,6 +10660,7 @@ with multiple R processes supported by the package @code{parallel}.") ("r-biocgenerics" ,r-biocgenerics) ("r-gdsfmt" ,r-gdsfmt) ("r-geoquery" ,r-geoquery) + ("r-illuminaio" ,r-illuminaio) ("r-methylumi" ,r-methylumi) ("r-minfi" ,r-minfi) ("r-watermelon" ,r-watermelon))) @@ -10645,14 +10674,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-seqbias (package (name "r-seqbias") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 - "06w43plv4x1pafybq633n7adqp9yj3bvaaamq7vylmkfbcx3nl8k")))) + "1q608c1madij8l52ljl3w52vi3cssr6ikny84yj6n8s7yvpx5jpr")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs @@ -10709,14 +10738,14 @@ injected in that sequence).") (define-public r-reqon (package (name "r-reqon") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 - "1z13avbxwvvhh03arjfnaipznynifsi8k2hzw4kappz24f7lwmza")))) + "14v79vg3pmpkbzgn8xqd020jdwcs8g57d46bzl23yi3w1rsfbrb1")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs @@ -10734,14 +10763,14 @@ format.") (define-public r-wavcluster (package (name "r-wavcluster") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 - "1sydzrqydfv1ik2h08xkxlx6xrv866bf0if6v5wch9l3krh0sych")))) + "1a1zhckrgq5yl51acj5piyh2hq70q6hhpym4cawzdssxhcbq70bk")))) (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs @@ -10781,14 +10810,14 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).") (define-public r-timeseriesexperiment (package (name "r-timeseriesexperiment") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TimeSeriesExperiment" version)) (sha256 (base32 - "1095a2ynxcf9xiac5cjzslcbmjnjpbby0vy7d84qagdiq1w6mrhn")))) + "0fphnkkd3i7zf33a9lhw95n80vzv1z7fmn7mhrfb949yz4jdvk7d")))) (properties `((upstream-name . "TimeSeriesExperiment"))) (build-system r-build-system) @@ -10822,14 +10851,14 @@ provides methods for retrieving enriched pathways.") (define-public r-variantfiltering (package (name "r-variantfiltering") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantFiltering" version)) (sha256 (base32 - "0abhrk53csd9jz9sv4q1qr74jax9mbj2icbz1iilf1123nvnjypd")))) + "15js8xzi9rsgkjkqcshzk3r3g85kdnxn5v2hi6l5s4yxj9lnq12p")))) (properties `((upstream-name . "VariantFiltering"))) (build-system r-build-system) @@ -10928,21 +10957,20 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "1pqy2g9pg8pswmkrs2fzlkwwliw2r7f33h05bci5bz41b8ribpzj")))) + "0f5y61dpzwmr8v7npim18zvxa8n49rbzclb9j72haba0px6ibhvw")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocparallel" ,r-biocparallel) - ("r-colorramps" ,r-colorramps) ("r-doparallel" ,r-doparallel) ("r-foreach" ,r-foreach) ("r-ggplot2" ,r-ggplot2) @@ -10952,9 +10980,11 @@ arrays based on fast wavelet-based functional models.") ("r-lme4" ,r-lme4) ("r-lmertest" ,r-lmertest) ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) ("r-pbkrtest" ,r-pbkrtest) ("r-progress" ,r-progress) ("r-reshape2" ,r-reshape2) + ("r-rlang" ,r-rlang) ("r-scales" ,r-scales))) (native-inputs `(("r-knitr" ,r-knitr))) @@ -10972,14 +11002,14 @@ measures.") (define-public r-htqpcr (package (name "r-htqpcr") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HTqPCR" version)) (sha256 (base32 - "1y3ik5a9w66jby6682jfm8mn2883s8yfv4xw8a8v1f6q2d1j938l")))) + "1d7qj5yv6kzqmdrnp5pd8qv1yr4bg8cs39p8ib0i0k8b4wr97kq3")))) (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs @@ -11006,14 +11036,14 @@ features (e.g. genes, microRNAs).") (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "unifiedWMWqPCR" version)) (sha256 (base32 - "1clcz610sl3s0mjf84j21xgrmjhkxcc4h292ljwq5yzbkk68g896")))) + "0kw26bm2yyna38q5r4zb2alpa3j4gx7v970419mnjlif4g0hmggk")))) (properties `((upstream-name . "unifiedWMWqPCR"))) (build-system r-build-system) @@ -11031,14 +11061,14 @@ data.") (define-public r-universalmotif (package (name "r-universalmotif") - (version "1.10.2") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "universalmotif" version)) (sha256 (base32 - "0hv2v2zgif5ihr5hxmdz32rln43jc1j0rslp44kd3rijjl45zysn")))) + "0d6zrwbc4i2npl29idm1icwa62wdx47z9s8yx7k662v3qagwpj16")))) (properties `((upstream-name . "universalmotif"))) (build-system r-build-system) @@ -11145,14 +11175,14 @@ cellular organization in health and disease.") (define-public r-bgmix (package (name "r-bgmix") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BGmix" version)) (sha256 (base32 - "1gp40ddspblpszzm4k4r7ysgx883iwdfqc5ds23p2q1ml9idwgvv")))) + "0x1sx319yfxgkscr9r62msq00ddvmzryzn42wy4dh5pvjmgifkkn")))) (properties `((upstream-name . "BGmix"))) (build-system r-build-system) (propagated-inputs @@ -11167,14 +11197,14 @@ gene expression.") (define-public r-bgx (package (name "r-bgx") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bgx" version)) (sha256 (base32 - "18n6j2ihv85rhai5sf5k3mwf9nkc2nl2sinx3rrs6sbl529g4mw4")))) + "0z3isnpyf9s11807dprxmd105lb0k4l7r1sygad30ncjvpldifzm")))) (properties `((upstream-name . "bgx"))) (build-system r-build-system) (propagated-inputs @@ -11192,14 +11222,14 @@ Affymetrix GeneChips.") (define-public r-bhc (package (name "r-bhc") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BHC" version)) (sha256 (base32 - "0aaawm7h3ppyyhd7hi14rpynagnxx4730f5vxizj5bpzwbclp6h9")))) + "09nw4ljc9sn7iw09ha0m614hmdjj193xhhav5x5p07l501kks6h2")))) (properties `((upstream-name . "BHC"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BHC/") @@ -11218,14 +11248,14 @@ algorithm which is more efficient for larger data sets.") (define-public r-bicare (package (name "r-bicare") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BicARE" version)) (sha256 (base32 - "0j3gs4xcdgaca2c62jf2h86skbbxm1c9g2khs5bsa8fmkskr6vl9")))) + "1g8vrsc05cysb36gsw8sfmr6dgbh4aji37vcq9qwkmkv3jgvnlf6")))) (properties `((upstream-name . "BicARE"))) (build-system r-build-system) (propagated-inputs @@ -11242,14 +11272,14 @@ results.") (define-public r-bifet (package (name "r-bifet") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiFET" version)) (sha256 (base32 - "1fwy7ws0bn67557s0kcw8pbln2jg834n6kfbs8297ps07nxr0lpj")))) + "0vidypvphnj76g4ra5ijrgqx2dnzw0fmvdvz35gsqswrr3k20jkk")))) (properties `((upstream-name . "BiFET"))) (build-system r-build-system) (propagated-inputs @@ -11272,14 +11302,14 @@ the read count and GC content bias.") (define-public r-rsbml (package (name "r-rsbml") - (version "2.50.0") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rsbml" version)) (sha256 (base32 - "017xwra6ms7kx6sg3ksw1vr9zn23imc2qjgpmjikx7mgbak125xh")))) + "0mdyr637sgasc156cv8i2s2mpl1hdvilfwwkhvw7l95pl90gnsh2")))) (properties `((upstream-name . "rsbml"))) (build-system r-build-system) (inputs @@ -11299,14 +11329,14 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") (define-public r-hypergraph (package (name "r-hypergraph") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hypergraph" version)) (sha256 (base32 - "01knpd964m2g9vwd7c72qnc8g2p2pzhvk7lin4mhvcmb3pvsdlh7")))) + "0xnyl9qh5p32ifvzkcl5g4a38zbnwykqzrp8gwz076a0ksiqqdxf")))) (properties `((upstream-name . "hypergraph"))) (build-system r-build-system) (propagated-inputs @@ -11321,14 +11351,14 @@ manipulating hypergraphs.") (define-public r-hyperdraw (package (name "r-hyperdraw") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hyperdraw" version)) (sha256 (base32 - "1qkxixkgvvfha0ii8rwwcbrbjmbbxsy8afv5ymcq01k3hbykx44r")))) + "1lkiqrk01hshms9ghsfynxwj69zr3463r3rg8rn7hkwn3bj8xyzj")))) (properties `((upstream-name . "hyperdraw"))) (build-system r-build-system) (inputs `(("graphviz" ,graphviz))) @@ -11345,14 +11375,14 @@ manipulating hypergraphs.") (define-public r-biggr (package (name "r-biggr") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiGGR" version)) (sha256 (base32 - "1y9659pxm65w51zvrz36girb3qvfc64zijjkxmg6xn4pbc8vv1wf")))) + "1g01666wwznk148776s4vr1hfi3dfl448dhgk4d1qy2wv6sxh9kr")))) (properties `((upstream-name . "BiGGR"))) (build-system r-build-system) (propagated-inputs @@ -11409,14 +11439,14 @@ a file-backed matrix with factor properties.") (define-public r-bigpint (package (name "r-bigpint") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigPint" version)) (sha256 (base32 - "0yrg9x1a92zmz7j5hk77cph1jg82mkpr7k7qi9fdr6z5nqq6fgz6")))) + "0b0l0v9p7a5da3x18d0pqn41ilgxfyzapjaawgsshcfm5mjq5d7q")))) (properties `((upstream-name . "bigPint"))) (build-system r-build-system) (propagated-inputs @@ -11452,14 +11482,14 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") (define-public r-chemminer (package (name "r-chemminer") - (version "3.44.0") + (version "3.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineR" version)) (sha256 (base32 - "1z59npqk7hnqzhjdnry6lfqlyxfzwqprp7bmbdzs4rp22pzcv1v8")))) + "069xd7if7fs69afmamgl6wrkzpnk97ic6z5ix4vvlzkb078dm0p8")))) (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs @@ -11471,11 +11501,13 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") ("r-dt" ,r-dt) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) + ("r-jsonlite" ,r-jsonlite) ("r-png" ,r-png) ("r-rcpp" ,r-rcpp) ("r-rcurl" ,r-rcurl) ("r-rjson" ,r-rjson) - ("r-rsvg" ,r-rsvg))) + ("r-rsvg" ,r-rsvg) + ("r-stringi" ,r-stringi))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/girke-lab/ChemmineR") @@ -11493,14 +11525,14 @@ structures.") (define-public r-bioassayr (package (name "r-bioassayr") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioassayR" version)) (sha256 (base32 - "1mlv80w8a7l8cii3dfqvanvh0qdqvcg8c1iiq4xlyvkjxfs64ka1")))) + "1nfp1alva6qim5rbhg9j9w97p2n4z21ghr4j489lqklkcs4d030f")))) (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs @@ -11528,14 +11560,14 @@ available bioactivity data.") (define-public r-biobroom (package (name "r-biobroom") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobroom" version)) (sha256 (base32 - "1ybyhmrcvj6k1laxw9bc8jbn533frkzh9k8kl1ibd5pi368rfqzn")))) + "034gbywrscv23kk1qnk7sc7dxdckmf60wh29fz65v1n28mkf180r")))) (properties `((upstream-name . "biobroom"))) (build-system r-build-system) (propagated-inputs @@ -11560,14 +11592,14 @@ visualize bioinformatics analyses.") (define-public r-graphite (package (name "r-graphite") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graphite" version)) (sha256 (base32 - "11bgz6951nfygxp3fm0190gf2bb5zplis1bc0am4757liw4qybhf")))) + "0wmdv4j6dinszxwpz2jddshkh1ahbhm2fxh6vhjsk4grw38i1lfr")))) (properties `((upstream-name . "graphite"))) (build-system r-build-system) (propagated-inputs @@ -11576,8 +11608,6 @@ visualize bioinformatics analyses.") ("r-graph" ,r-graph) ("r-httr" ,r-httr) ("r-rappdirs" ,r-rappdirs))) - (native-inputs - `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/graphite/") (synopsis "Networks from pathway databases") (description @@ -11589,14 +11619,14 @@ symbols).") (define-public r-reactomepa (package (name "r-reactomepa") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReactomePA" version)) (sha256 (base32 - "1293z89ai766c559axgr7mz5x4564gyl9xqzf6s8s0aj1xb35gqf")))) + "1f4kd5cql7knnqaq3ba48kkypw8p60lkfdsnpqxcabdj30gqp55b")))) (properties `((upstream-name . "ReactomePA"))) (build-system r-build-system) (propagated-inputs @@ -11621,14 +11651,14 @@ enrichment analysis and several functions for visualization.") (define-public r-ebarrays (package (name "r-ebarrays") - (version "2.56.0") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBarrays" version)) (sha256 (base32 - "1k1kl0m7wzaqpv7i20pfav2a6jf93bhri4w7qdikmvkf011n9422")))) + "10dw6c93rmpknzf4cnhw3y7lb27q4xq7x7wirl2a7qywdj0yj2g6")))) (properties `((upstream-name . "EBarrays"))) (build-system r-build-system) (propagated-inputs @@ -11667,13 +11697,13 @@ monograph.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "1h0l5w33c9jpc20pynq634qmx8jbfa802d7jslmf4haljmrxm4a1")))) + "0w9ddicyp9i8rxf92n9pghd9s6bb8jdjikaylrmkydhb7jbhan0y")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) @@ -11697,14 +11727,14 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-biocgraph (package (name "r-biocgraph") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocGraph" version)) (sha256 (base32 - "12bmj9kdlylp02cfwviak7y323ndccl2694rvi4cdg4vsx7v3ya3")))) + "0c7r0c1kx22dlwi6d1ldbkkbf53yi0p3vmgbwzrbkn3cina7bcxq")))) (properties `((upstream-name . "biocGraph"))) (build-system r-build-system) (propagated-inputs @@ -11722,13 +11752,13 @@ different graph related packages produced by Bioconductor.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.20.2") + (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "0p2wdq5vrx63ndghl9ww428z2lwnv5y88xmcr51by2g6vcj3brcf")))) + "0xx6xr01sb5wig94515zxgw24r9fv0g962ajy87741civhq32lbd")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) @@ -11750,13 +11780,13 @@ functionality.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.60.0") + (version "1.62.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "0pc5ll59vm8a9s1nrdc7p9wk11a52rrz669fsrrqd8qapa8p6wfd")))) + "1v6himzp546dpb990vv0nlya21w8x2x30137rsmahjzg942nzs9r")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -11778,14 +11808,14 @@ also known as views, in a controlled vocabulary.") (define-public r-experimenthub (package (name "r-experimenthub") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHub" version)) (sha256 (base32 - "1mzmw3100lf33yhz27nbxncrjk5bprlackrjcwf8xdhcaidg40p4")))) + "15las4qmqvrn81hczxa3ylikqh54kp1lg9r8rcyfvrx5l0kgwlfq")))) (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs @@ -11812,14 +11842,14 @@ access.") (define-public r-grohmm (package (name "r-grohmm") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "1h63vg1iskw79ijg5h1b9097ams8pp3kvnlawlfci6xfli07xpkj")))) + "1jcj29df4prknqwbydca1jb9w6njacjhwwk9jp0r5mvb88xrm60s")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs @@ -11839,14 +11869,14 @@ access.") (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiAssayExperiment" version)) (sha256 (base32 - "0l0arf3q1f6zy6pdgsy3h5n523sg1hlilv7lj7snr5814idgdj51")))) + "1h3b8vqlbd04amjprxd1814zksdrbi01a0xn3906vkbqi43hfyn9")))) (properties `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) @@ -11874,14 +11904,14 @@ rownames.") (define-public r-bioconcotk (package (name "r-bioconcotk") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocOncoTK" version)) (sha256 (base32 - "1ix09a39z7y2cj0y8qsd66ka8a8y8q79w08l4jv1yhhn9h4va89s")))) + "1h5s6wbc5n5x5d28rynxpcmaklxdhf72g9gg9fy8cg77niipvxd9")))) (properties `((upstream-name . "BiocOncoTK"))) (build-system r-build-system) (propagated-inputs @@ -11919,14 +11949,14 @@ tools for genome-scale analysis of cancer studies.") (define-public r-biocor (package (name "r-biocor") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioCor" version)) (sha256 (base32 - "135rga7mwpzy8ypvriqpbmlh9l5yf61s9s1sa9615qfab14jh06b")))) + "0ii4g7438lb34ykidkbxw3v3k289k662rgbgayf9gak5avpkb2cq")))) (properties `((upstream-name . "BioCor"))) (build-system r-build-system) (propagated-inputs @@ -11948,14 +11978,14 @@ gene selection, testing relationships, and so on.") (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.10.2") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "1sfp1nxlwbbbpx2iwvyk9p10jdy2vxhgn2b5fy5blayzjjlb3d80")))) + "13m6h35938407ajj7fakl50g4p2wsvinkg0r2mwl1zwq88735arg")))) (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) (propagated-inputs @@ -11996,14 +12026,14 @@ analytics on packages.") (define-public r-biocset (package (name "r-biocset") - (version "1.6.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSet" version)) (sha256 (base32 - "0nmrg9cgq8l9w467y364jghnvym05abpj8pyj90grmrib2xc5sj2")))) + "0ysm68gcalg3d91jx6vmdzra01vc6kvzqnvz557g3rnm0wkx12q6")))) (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs @@ -12034,14 +12064,14 @@ accessing web references for elements/sets are also available in BiocSet.") (define-public r-biocworkflowtools (package (name "r-biocworkflowtools") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocWorkflowTools" version)) (sha256 (base32 - "1a32bwgnxaw0gv2gij2p4rm0a6l06jjhidvfz2v4k900pz1w79av")))) + "1j9s8w5y8savcmh70npkanxacq1kipxnwk1wsiw5hwnp1p13ldaa")))) (properties `((upstream-name . "BiocWorkflowTools"))) (build-system r-build-system) @@ -12067,14 +12097,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") (define-public r-biodist (package (name "r-biodist") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioDist" version)) (sha256 (base32 - "1y1x9q9aa76gbhsyfn638rxp5icjvq30fv3a4205xh7g5jwlf6yw")))) + "0y35c9sdq5x4q64ip0wgqz59mh01l71k1pp6n8vqbr667nwg0gdp")))) (properties `((upstream-name . "bioDist"))) (build-system r-build-system) (propagated-inputs @@ -12090,14 +12120,14 @@ distance measures.") (define-public r-pcatools (package (name "r-pcatools") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PCAtools" version)) (sha256 (base32 - "11idi9fwvyhkakbm63qxcdhkany8gbskis04z0p5a39lppq8ks31")))) + "10kfhsxhsjpzal3yvcqg769h5fz99cqqjq217cj9jip3jfh2m2h4")))) (properties `((upstream-name . "PCAtools"))) (build-system r-build-system) (propagated-inputs @@ -12136,14 +12166,14 @@ dimensional mass cytometry data.") (define-public r-rgreat (package (name "r-rgreat") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGREAT" version)) (sha256 (base32 - "0ads9c9i8b39wvjih057zlyivj8zpsqjxf6r97yflz4sbi1jmcji")))) + "0kr61mhxp9phn1136fci450zwfhsipchmlm8d5rgib4lh0zbxrhl")))) (properties `((upstream-name . "rGREAT"))) (build-system r-build-system) (propagated-inputs @@ -12164,14 +12194,14 @@ user's input and automatically retrieving results from GREAT web server.") (define-public r-m3c (package (name "r-m3c") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "M3C" version)) (sha256 (base32 - "17gj4haa4ywc6bmppm342jzppl3inqa94235yspikij6c098vrmc")))) + "0jsql5wd58hs5mnn9wq5b4kl3z57y6amykirfb3k047zpyi8ijnh")))) (properties `((upstream-name . "M3C"))) (build-system r-build-system) (propagated-inputs @@ -12197,14 +12227,14 @@ hypothesis @code{K=1}.") (define-public r-icens (package (name "r-icens") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Icens" version)) (sha256 (base32 - "1rzgwxx4w2bqsaz0xmkhi4w9zsxgms80xf59zg1xp1camyhaihlz")))) + "08jd7g28mazvwd3qbq8y26czmkz45avp4vy8l7i5d6qajwzqzgzs")))) (properties `((upstream-name . "Icens"))) (build-system r-build-system) (propagated-inputs @@ -12222,14 +12252,14 @@ truncated data.") (define-public r-interval (package (name "r-interval") - (version "1.1-0.7") + (version "1.1-0.8") (source (origin (method url-fetch) (uri (cran-uri "interval" version)) (sha256 (base32 - "1b31lh0sv7lzy76230djipahxa10lblbr37kdiigr6hp3dd1xmz9")))) + "0g0k9nri19p3y3s70ic1w3i3sxq8fbsxaikd7c4d6afqzr8hk2nl")))) (properties `((upstream-name . "interval"))) (build-system r-build-system) (propagated-inputs @@ -12327,14 +12357,14 @@ generated.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "17a00blz4kvhmsk92bp5alj9kdpy7h1id7nk4vqxakhkb2jabr20")))) + "1i93vdqa6pwzamiryp3lv6cyvhx9shs01is0q6vbmdvcbii2vf3x")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) @@ -12348,13 +12378,13 @@ routines.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.30.1") + (version "0.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "103sw0fmmm4f3hprrsn7dwg0kmmr9mcmb46dcwwb6p5np0al2sfx")))) + "1zm1xlqrq1f9xa81j3ij2p78g3aywq7izsk3h40z94fjggahvc09")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -12415,14 +12445,14 @@ data manipulation and visualization.") (define-public r-rgraphviz (package (name "r-rgraphviz") - (version "2.36.0") + (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rgraphviz" version)) (sha256 (base32 - "0d0xq1vgr4b165cn4wg7zmfjyc1d9ir4amgs196j4cgrhpmrnl8s")))) + "0fyv1ybpahkwz3fawzxgxfnshi8y7c18262rgdmqwdl5662vv1p7")))) (properties `((upstream-name . "Rgraphviz"))) (build-system r-build-system) (arguments @@ -12453,13 +12483,13 @@ objects from the @code{graph} package.") (define-public r-fithic (package (name "r-fithic") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "1p8a6lis5yswaj647bjw89harlarnsxmvjzz63fn1l6gxrwhh8bx")))) + "0a3d2bxp98lmbf3i864zgfwxwvxyqfcrh75z9yz7ra7y44pkjr4y")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs @@ -12479,13 +12509,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "0s3kfqs3zlmq61hxdmxpmi9gfs9w3byckw7xzp1hrhdbsl46yvgq")))) + "1ckiwqfq86k8p3y36iwr7k3y6g4z80n8hb047c0i2491lrn23rhx")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs @@ -12508,14 +12538,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1718hplz5qlbwxwb87509bl7lir9kilvn1s7p2haz551pg48zvrc")))) + "13h6qr4zkynir0ck2aiasjvlid7hrk3m2lzkjyhpvbg1a15r8zi9")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs @@ -12539,14 +12569,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.14.2") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "1cwynbcaaxmbh45fc0d264liqdj0wbjlj7k2bsq3qfjbnh6kkam5")) + "0yly9s3wdnhd9ci2jxfkql38ibv35yzs38a6g6ashbg1m5kgwd9p")) (modules '((guix build utils))) (snippet '(begin @@ -12622,14 +12652,14 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.8.1") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "06bpfpddsl49csxrs8hlx5pv0absc2wdcparchf8qqaqydazwci2")))) + "1l8c9q35mf90ckb366bcfqa0v2gw7ahs2h362j7cwv8fp39h4mpb")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -12651,13 +12681,13 @@ matrices.") (define-public r-cner (package (name "r-cner") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CNEr" version)) (sha256 - (base32 "13w0gsfm7k29dp5nb0c9sb2ix506ph6dixsjis6xxcz6acq7lg2k")))) + (base32 "0w4iqmyyhsb6l9bi8c6qwdh4j6z2i1i5fi85ia9069fpl9d0hpl2")))) (properties `((upstream-name . "CNEr"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -12699,14 +12729,14 @@ advanced visualization of sets of conserved noncoding elements.") (define-public r-tfbstools (package (name "r-tfbstools") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TFBSTools" version)) (sha256 (base32 - "1avgjv2nyr28cla0z9dvh3v0hr1f561sz2as1k53a42irbjk0var")))) + "0j5gv145fczzdspwhbywlg47y05pgnkra9jg7bn4wa1k0cf5pr9g")))) (properties `((upstream-name . "TFBSTools"))) (build-system r-build-system) (propagated-inputs @@ -12745,14 +12775,14 @@ provides a wrapper of de novo motif discovery software.") (define-public r-motifmatchr (package (name "r-motifmatchr") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifmatchr" version)) (sha256 (base32 - "1vif3dp4lv4jz1pxsq0ig791ir8q65jmrlqmkyfxpfxfj5alqnbm")))) + "0f7j54zdn51h1gcn81vqs8avmschjwqprjcfpvsi00q4fna3fg7z")))) (properties `((upstream-name . "motifmatchr"))) (build-system r-build-system) (propagated-inputs @@ -12779,13 +12809,13 @@ This package wraps C++ code from the MOODS motif calling library.") (define-public r-chromvar (package (name "r-chromvar") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromVAR" version)) (sha256 - (base32 "1birmwvcvl2hb5ygbsb3wvbdfayqqs53j1bks46cbkq7ybigfyar")))) + (base32 "0ylsfr540l763bh010irbcavlskahyb1769pppimdgn22gyr3spk")))) (properties `((upstream-name . "chromVAR"))) (build-system r-build-system) (propagated-inputs @@ -12826,14 +12856,14 @@ sequence (@code{DNAse-seq}) experiments.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "1bwdhx0ss0s8f4xdgwd7x48apn849x4dyb5hbyglcz31r5vh1qgz")))) + "01075vbs8hy399pxalav9rbkz4djvl84ip559jkz51fypd0m4i39")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) @@ -12857,14 +12887,14 @@ libraries.") (define-public r-scuttle (package (name "r-scuttle") - (version "1.2.1") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "015k879gg2r39lp6mz26jwmysa56k0ial6v74zzmbi8hnz9zic3i")))) + "1dbdb6yc6wk01dljy1vy6f0lf44crc5rxxnc4bhjk8i4iljz8467")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs @@ -12892,13 +12922,13 @@ of other packages.") (define-public r-scater (package (name "r-scater") - (version "1.20.1") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "1046fgf93dda3y2z5ilrjdczz7klj67ag63p4p1h03965wpj9vfn")))) + "0k4i9pwmwxcr5a40ljl27wriccwn5vc52xy48yjjh8ppl5dbggdg")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -12910,6 +12940,7 @@ of other packages.") ("r-delayedmatrixstats" ,r-delayedmatrixstats) ("r-ggbeeswarm" ,r-ggbeeswarm) ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) ("r-gridextra" ,r-gridextra) ("r-matrix" ,r-matrix) ("r-rcolorbrewer" ,r-rcolorbrewer) @@ -12932,14 +12963,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.20.1") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "0ilzp6ngw9pq88gk79iic2zxfh5jaic6lnq3xfwc9a269bjylff0")))) + "1nyvbss4914giwzp5wiw9g4z5b6lr5iprbjrqlg4vpgnf1hz8k7l")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -12975,14 +13006,14 @@ variable and significantly correlated genes.") (define-public r-sparsematrixstats (package (name "r-sparsematrixstats") - (version "1.4.2") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sparseMatrixStats" version)) (sha256 (base32 - "0b22kzg751zlkcbs8pi0bcqrsj3imsg35qfvxfrqb7gav7qznc8v")))) + "0ifqj4a6mn4749sr62gq3dwd6mmbbzdx5mh5b5663vcgl1kw96x1")))) (properties `((upstream-name . "sparseMatrixStats"))) (build-system r-build-system) @@ -13003,14 +13034,14 @@ data in the column sparse format.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.14.3") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1zxs2wjnsq9w1cl4andsd7y9xsdnl1an55khw9viaq758m7hhbcn")))) + "1pqwkk39rfhcnhmgchk0gfmm4jgasl19yq0nhhwsfj45y2vk6kjk")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) @@ -13039,14 +13070,14 @@ memory usage and processing time is minimized.") (define-public r-mscoreutils (package (name "r-mscoreutils") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsCoreUtils" version)) (sha256 (base32 - "13g8a726vsyjs6m1kd42vf8avdnmhykxhl6z3j2njzkp2jg17pd8")))) + "1w8d1v2r3plwwcz23zhbpvklhapf2a6x3xmglyh4sh6sy9ynkgrv")))) (properties `((upstream-name . "MsCoreUtils"))) (build-system r-build-system) (propagated-inputs @@ -13068,17 +13099,49 @@ well as misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages.") (license license:artistic2.0))) +(define-public r-msfeatures + (package + (name "r-msfeatures") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MsFeatures" version)) + (sha256 + (base32 "020ifrijlzdd3qk4bhd9z4knj5d87ildrkl3wcmxvwkvs9rbh8rq")))) + (properties `((upstream-name . "MsFeatures"))) + (build-system r-build-system) + (propagated-inputs + `(("r-mscoreutils" ,r-mscoreutils) + ("r-protgenerics" ,r-protgenerics) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/RforMassSpectrometry/MsFeatures") + (synopsis "Functionality for mass spectrometry features") + (description + "The MsFeature package defines functionality for Mass Spectrometry +features. This includes functions to group (LC-MS) features based on some of +their properties, such as retention time (coeluting features), or correlation +of signals across samples. This packge hence allows to group features, and +its results can be used as an input for the @code{QFeatures} package which +allows to aggregate abundance levels of features within each group. This +package defines concepts and functions for base and common data types, +implementations for more specific data types are expected to be implemented in +the respective packages (such as e.g. @code{xcms}).") + (license license:artistic2.0))) + (define-public r-biocio (package (name "r-biocio") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocIO" version)) (sha256 (base32 - "0skwnpxl6fkqihidpqrfzzh7b05x11j6jwkiinmhggmv0ggjb5ph")))) + "1qg6v961sbj7qwyjx4z720f6h0kq693p7gc8q99my7gqkbbcxrfr")))) (properties `((upstream-name . "BiocIO"))) (build-system r-build-system) (propagated-inputs @@ -13105,14 +13168,14 @@ as well as local access. Developers can register a file extension, e.g., (define-public r-msmseda (package (name "r-msmseda") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsEDA" version)) (sha256 (base32 - "0555a3riyp781mlffmnf93igfq8vl8wjk51pa9qb48qkdn6y8pfc")))) + "1jammjkjjkcqad2ki02l2pdf4jybyh71hv463aya2ylmzsin5vi9")))) (properties `((upstream-name . "msmsEDA"))) (build-system r-build-system) (propagated-inputs @@ -13131,14 +13194,14 @@ experiments, and visualize de influence of the involved factors.") (define-public r-msmstests (package (name "r-msmstests") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsTests" version)) (sha256 (base32 - "11vhy1l6za73dpdj85q4ksaghgd8vb2h8v9iirmsn2vpajqrvgjh")))) + "0xmjgd8rqpb8i7d46pvnj7da2di8bwfdncr48b8hgylkc98ghznb")))) (properties `((upstream-name . "msmsTests"))) (build-system r-build-system) (propagated-inputs @@ -13163,14 +13226,14 @@ relevant, and the minimum expression of the most abundant condition.") (define-public r-catalyst (package (name "r-catalyst") - (version "1.16.2") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CATALYST" version)) (sha256 (base32 - "1vw8x54hwgcyn29k81zcvawawy2iy2qgp49gjpb830q04gx6yc6h")))) + "15lah45lf16zh1ankbpjvz8zp38lldvq074nmvb99rhhqys2gbgi")))) (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs @@ -13221,14 +13284,14 @@ standards, ii) single-cell deconvolution, and iii) bead-based compensation.") (define-public r-erma (package (name "r-erma") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "02a9702sasgighwb0f9ii8n30ngfx1hjnppaay1f5zsigr8vqalz")))) + "0pb9ar1wy613vg6sfdmn8n4cfv1328m8bagnigsjdb3hc3hbir4z")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -13261,14 +13324,14 @@ by Ernst and Kellis.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "0k3dxacrwgyrkvm7ggc2s1s1pbfs6c0a7ngykkj7jnc73czvnilx")))) + "1svmjaa3gisi39sl52337drvd54havcy5pjmwrykgykz5flid2m7")))) (build-system r-build-system) (arguments `(#:phases @@ -13429,14 +13492,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.36.2") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0lp0k8jd4dfsfn10706124graaqnzcyv1siblvm8dn2ykw2rc6vl")))) + "0nqa7m300d7gpsayb6c6rv64d3y8c390wvwgz7v29zs9c025s9a8")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -13478,14 +13541,14 @@ with your data.") (define-public r-gwascat (package (name "r-gwascat") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "0109cxsviq1sk5hfwkjzd0y1kpm934287asjjd0j8jhh4b0ah2b2")))) + "0s67jgk3gnfiyfjwhq4r5xlfnip29blis4fg75kn4qmvjv5j2pxx")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -13512,13 +13575,13 @@ EMBL-EBI GWAS catalog.") (define-public r-kegggraph (package (name "r-kegggraph") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGgraph" version)) (sha256 - (base32 "0zxdph5hzr3kzj2g1mjqpiviwa189a5sq4bw7wiry6r79fdnklqs")))) + (base32 "1qqvbv1sq9j570syb2802ya2ffg1k8f1w986wr6ksqkwxb9qbbm4")))) (properties `((upstream-name . "KEGGgraph"))) (build-system r-build-system) (propagated-inputs @@ -13539,14 +13602,14 @@ functionalities including parsing, graph operation, visualization and etc.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.22.1") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "16vp5psmigxdkkd6fbivb6s8mvd7rsnm771wsbjvayl2y7ig7kq4")))) + "1v9b372d5hpwwik6956mfwc9b3bibygz042i4nydsklnbwm5vcmg")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -13665,13 +13728,13 @@ other functional sequencing data.") (define-public r-pathview (package (name "r-pathview") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pathview" version)) (sha256 - (base32 "1fank0qavv9ikmzxvms8mky2wbzny02rfqkvsqzma26r3vl4r1g1")))) + (base32 "1jdl81lvrsz03b1nws90nssf2clipipzaqvwm1pq57mvshnlnkjr")))) (properties `((upstream-name . "pathview"))) (build-system r-build-system) (propagated-inputs @@ -13699,14 +13762,14 @@ large-scale and fully automated analysis.") (define-public r-snpstats (package (name "r-snpstats") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "11vvih5y9kvyjfp2navkfpp4xiyfgwlv4r0x3p52hkj92pc2pg3g")))) + "0ha34b5cg26940xihgky45adns1nflrgq2qjq77w4bncxpaacsqq")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -13726,14 +13789,14 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.") (define-public r-chromstar (package (name "r-chromstar") - (version "1.18.0") + (version "1.19.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromstaR" version)) (sha256 (base32 - "09cqzylci4x4i7wn4ckcqhdlljbzfrp08wdvkkc5vrdldnj9pq5h")))) + "0z511l26fhz00qn8h2yybylk8c3ws8hj1hp8hq9qj9mfczwiqy3j")))) (properties `((upstream-name . "chromstaR"))) (build-system r-build-system) (propagated-inputs @@ -13764,14 +13827,14 @@ analyses.") (define-public r-guitar (package (name "r-guitar") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Guitar" version)) (sha256 (base32 - "1q4m6c5181dw12lvdp324jlk78c9jgcsg6b9hk87zjadp6j0gfr6")))) + "082yja4mmsq77sllv3c88agxjbb6jxwil2krb8fkfsijvyyx11c9")))) (properties `((upstream-name . "Guitar"))) (build-system r-build-system) (propagated-inputs @@ -13796,13 +13859,13 @@ starting site, start codon, stop codon and transcription ending site.") (define-public r-sushi (package (name "r-sushi") - (version "1.30.0") + (version "1.31.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Sushi" version)) (sha256 (base32 - "1m5l0nflhcynb3gz7b8qzvknb0s6xhds8z1yl3mbv8ic9qn2knv4")))) + "1cj4palsq99vnwihp6z9mw0f8w9qj2vq8zwnabf3bgg0l1wpsc7c")))) (properties `((upstream-name . "Sushi"))) (build-system r-build-system) (propagated-inputs @@ -13818,14 +13881,14 @@ visualizations for publication-quality multi-panel figures.") (define-public r-ballgown (package (name "r-ballgown") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ballgown" version)) (sha256 (base32 - "0ff8z4pfgzai2q4aafclg36bhsi9jwl9xhh1p9fqhmikisscq7i1")))) + "0fiky82arvgzgxrm4bqn74m5kngqpdaqf6ks4cr89nlnhfq0v6rf")))) (properties `((upstream-name . "ballgown"))) (build-system r-build-system) (propagated-inputs @@ -13852,14 +13915,14 @@ to annotation.") (define-public r-megadepth (package (name "r-megadepth") - (version "1.2.3") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "megadepth" version)) (sha256 (base32 - "0grgj7bzyqnxby0sx5ic1h9bzmx19xwl0a5b3v6wbnwqcla2i3kg")))) + "0mg7n3990qv65rg624473ssccka0yjpgc20glrdc5saci891j44r")))) (properties `((upstream-name . "megadepth"))) (build-system r-build-system) (inputs `(("megadepth" ,megadepth))) @@ -13885,14 +13948,14 @@ regions or annotations of your choice from BigWig files.") (define-public r-beclear (package (name "r-beclear") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BEclear" version)) (sha256 (base32 - "0w18livng2gcmjgvws7pix3gsnj237rs34sgwxsfmn8p5vfx8b30")))) + "1njb1lfd4wmsrfw06jc8z8vdk14nmcw9lwyvbxr7z1zg4h8v6c29")))) (properties `((upstream-name . "BEclear"))) (build-system r-build-system) (propagated-inputs @@ -13918,14 +13981,14 @@ real numbers.") (define-public r-bgeecall (package (name "r-bgeecall") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeCall" version)) (sha256 (base32 - "1byciy7vzbdkdgaim10s9qb7zlxsywbhcsrka31gm0rm9ljqc665")))) + "0rbbl8m48qcvl26lnf27jq108p7pi84m9ac3qcpjc0ax5wywbv16")))) (properties `((upstream-name . "BgeeCall"))) (build-system r-build-system) (propagated-inputs @@ -13954,14 +14017,14 @@ all RNA-Seq libraries of each species integrated in Bgee.") (define-public r-bgeedb (package (name "r-bgeedb") - (version "2.18.1") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeDB" version)) (sha256 (base32 - "1ziq180yfpdqwhjdzkwjjhwzn3kb0gkj6q0a26c7a30mcfb50w11")))) + "0pjymal01sjl5dc37g66wykgxnksarlbvwnbvhg7w0i7y92zavqk")))) (properties `((upstream-name . "BgeeDB"))) (build-system r-build-system) (propagated-inputs @@ -13988,14 +14051,14 @@ anatomical terms, mapped to genes by expression patterns.") (define-public r-biobtreer (package (name "r-biobtreer") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobtreeR" version)) (sha256 (base32 - "0pynx4ps1qxsn13ba6zyg6h5dqlp2y7qish67m7sdjns079zh061")))) + "0m9gx2g5ishbbh7aqp09mpknhr7q1v5ap0s6xp6ccj01pz2gkk8s")))) (properties `((upstream-name . "biobtreeR"))) (build-system r-build-system) (propagated-inputs @@ -14015,14 +14078,14 @@ mappings functionalities.") (define-public r-minet (package (name "r-minet") - (version "3.50.0") + (version "3.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minet" version)) (sha256 (base32 - "0bir2zr4r2wawkdvdhrk2hcyxmgkrkfvx36jj85fcm24axlqrzzb")))) + "0nhgvgci4r9pjfsnvxyj2q8im1wvig4zmfx2kidw8f63x2ip2rbd")))) (properties `((upstream-name . "minet"))) (build-system r-build-system) (propagated-inputs @@ -14037,14 +14100,14 @@ information networks from data.") (define-public r-genetclassifier (package (name "r-genetclassifier") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geNetClassifier" version)) (sha256 (base32 - "1i1cavbbvxzqgqxfmikghnls18jrq12hb953mjrwa95lkhzdxm2d")))) + "1phyphdc1i55ab1a05633b0p41q8n7w0byp1plgcav2s3h8mk1km")))) (properties `((upstream-name . "geNetClassifier"))) (build-system r-build-system) @@ -14065,14 +14128,14 @@ interface to query the classifier.") (define-public r-dir-expiry (package (name "r-dir-expiry") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dir.expiry" version)) (sha256 (base32 - "05mk7iwzay1xrgvssbz7nyl5d1n03syalbk18lmjmbx05dy0cjik")))) + "1bwmlxmizhmim2l0mk406hxfr5mnmsg5zbqkjyygaipa971m9s00")))) (properties `((upstream-name . "dir.expiry"))) (build-system r-build-system) (propagated-inputs `(("r-filelock" ,r-filelock))) @@ -14089,14 +14152,14 @@ eliminating obsolete caches generated by old versions of packages.") (define-public r-basilisk-utils (package (name "r-basilisk-utils") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk.utils" version)) (sha256 (base32 - "0qbm6rj6h059hakflbwz4j4f59311jhbk5dnpx11kyixh5pgjk7v")))) + "0578rq2yz24sv7anb7vp0a0y35944ag1l8ca6haanb03wl97wm99")))) (properties `((upstream-name . "basilisk.utils"))) (build-system r-build-system) @@ -14113,14 +14176,14 @@ package, primarily for creation of the underlying Conda instance.") (define-public r-basilisk (package (name "r-basilisk") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk" version)) (sha256 (base32 - "1nzbn3f2jzvg3a3m6wgksi4cvamqas2q7csdk4ir7fcirasf536v")))) + "1cdkpngv9qybd9yxc3i2201p433vkkahs71v28x6lgs5l2wz3m1a")))) (properties `((upstream-name . "basilisk"))) (build-system r-build-system) (propagated-inputs @@ -14141,16 +14204,21 @@ Python environments in a single R session.") (define-public r-biocthis (package (name "r-biocthis") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocthis" version)) (sha256 (base32 - "08awghsg7q22csb0j9dr8dpb1vkn9gcs9qnhhljxifkw2ahbqia4")))) + "0kh5lmv992v4r5r58x29403cll0zxr9fx4ar81nrzvnch5668v39")))) (properties `((upstream-name . "biocthis"))) (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs `(("r-biocmanager" ,r-biocmanager) ("r-fs" ,r-fs) @@ -14170,14 +14238,14 @@ Bioconductor-friendly.") (define-public r-biocdockermanager (package (name "r-biocdockermanager") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocDockerManager" version)) (sha256 (base32 - "0dh1flm5chsdcihljrg6znjskqkp0qyjh39hsv4zq0frf1rm97j7")))) + "1kpdmpcngnl667bfffp9bkf8c31ipmhsncq0h9bf3a4k8b83pi0w")))) (properties `((upstream-name . "BiocDockerManager"))) (build-system r-build-system) @@ -14200,18 +14268,19 @@ the Bioconductor project.") (define-public r-biodb (package (name "r-biodb") - (version "1.0.4") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biodb" version)) (sha256 (base32 - "1apnbr5p619nsrhd2drm6arj69sw0wijv8ap7dfrndqkffrpbfmx")))) + "0q343zbx341xdy634p50k7bj6byv8v2rqzy50nw75a79206pajl4")))) (properties `((upstream-name . "biodb"))) (build-system r-build-system) (propagated-inputs - `(("r-chk" ,r-chk) + `(("r-biocfilecache" ,r-biocfilecache) + ("r-chk" ,r-chk) ("r-jsonlite" ,r-jsonlite) ("r-lgr" ,r-lgr) ("r-lifecycle" ,r-lifecycle) @@ -14244,14 +14313,14 @@ separate published packages.") (define-public r-biomformat (package (name "r-biomformat") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomformat" version)) (sha256 (base32 - "1wgshkddxbmpsihpkm0dp7vqp59ns6iqbx574y80n2pxb8dx8sy9")))) + "0xf99j4lhf8kh9h1317hrbzxdv6rljs1fn68r8s40x6y4db3l817")))) (properties `((upstream-name . "biomformat"))) (build-system r-build-system) (propagated-inputs @@ -14276,14 +14345,14 @@ as extensions of common core functions/methods.") (define-public r-mvcclass (package (name "r-mvcclass") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MVCClass" version)) (sha256 (base32 - "1di7y10mr7caacd6igwxnr62cm4v1x877yi4a2i5jqz1058jqni7")))) + "088gzh33vjkjf78xczqfs89pyg0k7c3533yfvijqxl84ni2ky78z")))) (properties `((upstream-name . "MVCClass"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/MVCClass") @@ -14296,14 +14365,14 @@ design.") (define-public r-biomvcclass (package (name "r-biomvcclass") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioMVCClass" version)) (sha256 (base32 - "04pld93nffbci47dnf0awmcmhlfzv599ggcd7hvq78w41ac60qv8")))) + "0jqgazwz35gz11a7vzanyy2yalzalx0z0rw6y18nmk8dbv01nv2j")))) (properties `((upstream-name . "BioMVCClass"))) (build-system r-build-system) (propagated-inputs @@ -14321,14 +14390,14 @@ design.") (define-public r-biomvrcns (package (name "r-biomvrcns") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomvRCNS" version)) (sha256 (base32 - "0wyzj422smr4m9mswzn9inc1sn86pnia7jmd6k28nd2a7fjyrm16")))) + "01nhjhfyzs67p97bk9bjqdxk239ckl8sgfj55azk1zmw92aw2hfy")))) (properties `((upstream-name . "biomvRCNS"))) (build-system r-build-system) (propagated-inputs @@ -14349,14 +14418,14 @@ using aCGH or sequencing.") (define-public r-bionero (package (name "r-bionero") - (version "1.0.4") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNERO" version)) (sha256 (base32 - "1yj0pavyfrj2gsvaj1dkgmznibm2appxjx9rk5qjslhslmm5b05b")))) + "0ddrzv1g46hvm52dzrcj5nbyyw9a16cqk8zg20wnkrh3qw1h4d9p")))) (properties `((upstream-name . "BioNERO"))) (build-system r-build-system) (propagated-inputs @@ -14405,14 +14474,14 @@ networks.") (define-public r-bionet (package (name "r-bionet") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNet" version)) (sha256 (base32 - "15rk1jfv4h1mxvr5bs0qmq6fdnza7zcmksigqxb46fs7f6znr3yi")))) + "05rj14jn4gn0hfn57amf19b8fqwkd3y2ji3mg7m1yg1w7n4qxqsg")))) (properties `((upstream-name . "BioNet"))) (build-system r-build-system) (propagated-inputs @@ -14438,14 +14507,14 @@ scoring subnetwork.") (define-public r-bionetstat (package (name "r-bionetstat") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNetStat" version)) (sha256 (base32 - "16xlfng9m8xvm831c2x6zmjc0gavlfiy9pnza55hdv86888fcnbg")))) + "13br8x4809hrr4ibz6iy5qjza9j6cazmkpvfikvw6bs588csxwf8")))) (properties `((upstream-name . "BioNetStat"))) (build-system r-build-system) (propagated-inputs @@ -14480,14 +14549,14 @@ network and metabolic pathways view.") (define-public r-bioqc (package (name "r-bioqc") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioQC" version)) (sha256 (base32 - "04akp94p0d0zid55m1b1k3qlw7iq914pcg57lihgj3pa92n1sc5l")))) + "190336qk0plg79gzvfn6wfplsi8nq0nj8508g7m0w3z6bdgwy407")))) (properties `((upstream-name . "BioQC"))) (build-system r-build-system) (propagated-inputs @@ -14508,14 +14577,14 @@ optimised for high performance.") (define-public r-biotip (package (name "r-biotip") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioTIP" version)) (sha256 (base32 - "1i6r8px0fmdjx8frpljppwql74mhx08ibvhs9y3qk91ck5h3f0js")))) + "0xmy5c4i9gf6d04gara6lbnnldqmzjaascb2pd2ih60jw2mvl4ys")))) (properties `((upstream-name . "BioTIP"))) (build-system r-build-system) (propagated-inputs @@ -14538,24 +14607,22 @@ help unravel disease regulatory trajectory.") (define-public r-biotmle (package (name "r-biotmle") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biotmle" version)) (sha256 (base32 - "01smkmbv40yprgrgi2gjnmi8ncqyrlkfdxsh33ki20amcx32nc7f")))) + "0p3iavf9059qa8qvfvqzskfc5gki3z0ivkkqdwg5anvf0wv2k47g")))) (properties `((upstream-name . "biotmle"))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) - ("r-dofuture" ,r-dofuture) ("r-dplyr" ,r-dplyr) ("r-drtmle" ,r-drtmle) - ("r-future" ,r-future) ("r-ggplot2" ,r-ggplot2) ("r-ggsci" ,r-ggsci) ("r-limma" ,r-limma) @@ -14582,14 +14649,14 @@ ensemble machine learning for the estimation of nuisance functions.") (define-public r-bsseq (package (name "r-bsseq") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bsseq" version)) (sha256 (base32 - "1xpv85hr681kkkilsnasndkszwmzbzq11y0lff4na2ilsm7sqmmi")))) + "1i30zf6457a0qd64s89x9l544y1h0hj9rfgf1m8l4krd487a9b9d")))) (properties `((upstream-name . "bsseq"))) (build-system r-build-system) (propagated-inputs @@ -14628,14 +14695,14 @@ visualizing bisulfite sequencing data.") (define-public r-dmrseq (package (name "r-dmrseq") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dmrseq" version)) (sha256 (base32 - "1jbbjifjsnk9261wqmdwkbzj1w52g6vaanpk4w816ri0fap587m4")))) + "1d6y6rbvcgprmzqkdzxg5csf0yv845d9vw10pcd1pzyndrama1vd")))) (properties `((upstream-name . "dmrseq"))) (build-system r-build-system) (propagated-inputs @@ -14674,13 +14741,13 @@ interest on transformed methylation proportions.") (define-public r-omnipathr (package (name "r-omnipathr") - (version "3.0.4") + (version "3.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OmnipathR" version)) (sha256 - (base32 "0rbq3h3cp5dgpy5ifmbnfm6z8w4jv45wjzyl1f4qacgrbyf2l30a")))) + (base32 "1q89mxnp8cig9r1499g7fb9p9x9ryz1dmc3w6ps5ww9n6rl8jqk8")))) (properties `((upstream-name . "OmnipathR"))) (build-system r-build-system) (arguments @@ -14690,6 +14757,7 @@ interest on transformed methylation proportions.") (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs `(("r-checkmate" ,r-checkmate) + ("r-crayon" ,r-crayon) ("r-curl" ,r-curl) ("r-digest" ,r-digest) ("r-dplyr" ,r-dplyr) @@ -14725,14 +14793,14 @@ for ligand activity prediction from transcriptomics data.") (define-public r-biscuiteer (package (name "r-biscuiteer") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biscuiteer" version)) (sha256 (base32 - "0f4kk4v2c5diq0fbvyvgwjd1kjk9izr6n9wfrlrr7wbx4pz3c3h6")))) + "16ds322b21g8ys5c3lkrvi70i82f9rxvnknbiqx4sp6f2l01j5yj")))) (properties `((upstream-name . "biscuiteer"))) (build-system r-build-system) (propagated-inputs @@ -14776,14 +14844,14 @@ estimates, etc.") (define-public r-tximeta (package (name "r-tximeta") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 - "0ipgpcl93cac4qff6lp9x2l3gav5kb1x1d56g32h09hlm797rvvh")))) + "03fbz6pka7bcbhd0bblgckyxsqhzp4n8qp2dcpdb3sr01lyw4bc5")))) (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs |