diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 69 |
1 files changed, 48 insertions, 21 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d84481bdb8..35fb43b3cd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1946,13 +1946,13 @@ microarrays.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.54.0") + (version "1.54.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "117zh7iqa6phsrxrkv45kxraamm3vbfz5i1a8vkhyalhdbs5ssph")))) + "0fcammls431pgmp47r85k0zh3bz42bajbqdmafd31kpqncc1ijal")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -2154,13 +2154,13 @@ on Bioconductor or which replace R functions.") (define-public r-biomart (package (name "r-biomart") - (version "2.48.0") + (version "2.48.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "1h8lzd63qvy1y75nlnhazpkyhl6g1hz80baqg20gpxbv38wkyf55")))) + "1a1lh0z1vk1q3wil85pi7v0f9miv070sjkbnwbw390zvncwakqxa")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -2172,7 +2172,8 @@ on Bioconductor or which replace R functions.") ("r-progress" ,r-progress) ("r-rappdirs" ,r-rappdirs) ("r-stringr" ,r-stringr) - ("r-xml" ,r-xml))) + ("r-xml" ,r-xml) + ("r-xml2" ,r-xml2))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/biomaRt") @@ -2246,13 +2247,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.60.0") + (version "2.60.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "0xidh6wp0l47g1j9x8d4fs91ky6pi5nzf85ry801gqd2gqajh2zy")))) + "1a2vq4rram7chnccx0piccgi0mlblmjh26y51bch86lxr7qwlr22")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -4764,14 +4765,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.2.1") + (version "3.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "12x80z1a8gihqrlaxmzk80nc5700la72lival58s4wjv4k2lhyf3")))) + "037z4mm8q5c50lwf63l1gmksd9fzfmyyp259jncpsxa3almf5jgh")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs @@ -5779,14 +5780,14 @@ missing values and weighting where appropriate.") (define-public r-biocsingular (package (name "r-biocsingular") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 - "1l0xgc3z5ci5sid198nsgg0k5i40rh877jybzmy0ify7rzv8carp")))) + "16gkwq8fb8jdchpnlzq2hz3i74a6pzbnc1bf93282h11mp7qr58l")))) (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs @@ -7162,14 +7163,14 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "0nvjwwzpmhsfkxqrn8v1a1wcrvr3xl1wn5dy89vsrdydyv31gdc6")))) + "116mwmpr06f4z60avdsfzdalbxn4119dbzk3jz1q5fp81qvw164d")))) (build-system r-build-system) (propagated-inputs `(("r-cowplot" ,r-cowplot) @@ -9948,6 +9949,32 @@ each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. genes in the gene-set that are ranked above the leading edge).") (license license:gpl3))) +(define-public r-chicago + (package + (name "r-chicago") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Chicago" version)) + (sha256 + (base32 + "0dkwy6pfvzd7g4qmhjl24ypn92l78w1zy0ajhcxgg39f7zsq883x")))) + (properties `((upstream-name . "Chicago"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-delaporte" ,r-delaporte) + ("r-hmisc" ,r-hmisc) + ("r-mass" ,r-mass) + ("r-matrixstats" ,r-matrixstats))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/Chicago") + (synopsis "Capture Hi-C analysis of genomic organization") + (description + "This package provides a pipeline for analysing Capture Hi-C data.") + (license license:artistic2.0))) + (define-public r-cicero (package (name "r-cicero") @@ -11389,13 +11416,13 @@ different graph related packages produced by Bioconductor.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.20.0") + (version "2.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "062zhy33a2c70ibqghnjxcys0wbqc998aza8nnygk4zmpd4iyy1z")))) + "0gkprmilj6lwnyghpyfzkwmfl3gva75lgpn4ck8jgikqac8jcq0x")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) @@ -12207,14 +12234,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "1ypqmd4nz4hxlb2qsay7f5784dqdjhc3b19pckzkhb65bfycdn87")) + "0ld1p3rxsx47bdq2wz9110zvwhabsnn92wkhz8x7xzfr01cc9glm")) (modules '((guix build utils))) (snippet '(begin @@ -12560,13 +12587,13 @@ of other packages.") (define-public r-scater (package (name "r-scater") - (version "1.20.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "0rppbd0mfyi41wb56i499mk3nj2ljhgnv3bv0k2p31bngvmb03j5")))) + "1046fgf93dda3y2z5ilrjdczz7klj67ag63p4p1h03965wpj9vfn")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -13097,14 +13124,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.36.0") + (version "1.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "19vjf4sdz5sxbcdilsqx7m57fq5a8xnxjf354zx2l5mgjrkzkk3h")))) + "1mljj70pg36dgrqhdfj643p39wbps66zz23xw6km150lq6fpgpg5")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs |