From 49e8978452b821dc42e257d6e0c56879c3090b3b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 17 Jun 2021 14:24:35 +0200 Subject: gnu: r-annotationdbi: Update to 1.54.1. * gnu/packages/bioconductor.scm (r-annotationdbi): Update to 1.54.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d84481bdb8..234ae1d7e3 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) -- cgit v1.2.3 From 495a9cff6dc0cb68d579c20bfca9f090672442ca Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 17 Jun 2021 14:24:41 +0200 Subject: gnu: r-biomart: Update to 2.48.1. * gnu/packages/bioconductor.scm (r-biomart): Update to 2.48.1. [propagated-inputs]: Add r-xml2. --- gnu/packages/bioconductor.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 234ae1d7e3..28375da78a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -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") -- cgit v1.2.3 From 005d3d405831cb312105f507dcc1e325806604b1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 17 Jun 2021 14:24:41 +0200 Subject: gnu: r-biostrings: Update to 2.60.1. * gnu/packages/bioconductor.scm (r-biostrings): Update to 2.60.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 28375da78a..fee2b0bc62 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2247,13 +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) -- cgit v1.2.3 From 79b67d2f546be5409b9463b731fc21d981b0b90b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 17 Jun 2021 14:24:41 +0200 Subject: gnu: r-diffbind: Update to 3.2.2. * gnu/packages/bioconductor.scm (r-diffbind): Update to 3.2.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fee2b0bc62..8a2767bc47 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4765,14 +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 -- cgit v1.2.3 From c5b7ade1c6b0a2586a7e72b9e68380a28ba6c198 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 17 Jun 2021 14:24:41 +0200 Subject: gnu: r-biocsingular: Update to 1.8.1. * gnu/packages/bioconductor.scm (r-biocsingular): Update to 1.8.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8a2767bc47..21cb6b7939 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5780,14 +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 -- cgit v1.2.3 From 46178051d5d62fddb981931b2d1b0e300a83a099 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 17 Jun 2021 14:24:41 +0200 Subject: gnu: r-enrichplot: Update to 1.12.1. * gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.12.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 21cb6b7939..5863a6480a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7163,14 +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) -- cgit v1.2.3 From e4c21552639dc1d14df13d73178c671c5dc536ba Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 17 Jun 2021 14:24:41 +0200 Subject: gnu: r-biocstyle: Update to 2.20.1. * gnu/packages/bioconductor.scm (r-biocstyle): Update to 2.20.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5863a6480a..2d6929f916 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11390,13 +11390,13 @@ 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) -- cgit v1.2.3 From 06fb533c28c92572dee0a67e1adc86d8f82f7c02 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 17 Jun 2021 14:24:41 +0200 Subject: gnu: r-rhdf5lib: Update to 1.14.1. * gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.14.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2d6929f916..700795421b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12208,14 +12208,14 @@ 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 -- cgit v1.2.3 From 45f1e079a59091b4536f974a6356ddbc4b58ef8a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 17 Jun 2021 14:24:42 +0200 Subject: gnu: r-scater: Update to 1.20.1. * gnu/packages/bioconductor.scm (r-scater): Update to 1.20.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 700795421b..5216fdd859 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -12561,13 +12561,13 @@ 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) -- cgit v1.2.3 From 88d8b4ece08a54fe7596c38fee860b5ee95e6565 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 17 Jun 2021 14:24:42 +0200 Subject: gnu: r-gviz: Update to 1.36.1. * gnu/packages/bioconductor.scm (r-gviz): Update to 1.36.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5216fdd859..c5509dcb69 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -13098,14 +13098,14 @@ 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 -- cgit v1.2.3 From ef5468ff0ed2f943cae8d3dece0e964e295b533a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 17 Jun 2021 14:57:47 +0200 Subject: gnu: Add r-chicago. * gnu/packages/bioconductor.scm (r-chicago): New variable. --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c5509dcb69..35fb43b3cd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9949,6 +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") -- cgit v1.2.3