From 5b98473a1ffa84b27df292b3190b31e07441cb67 Mon Sep 17 00:00:00 2001 From: Vagrant Cascadian Date: Fri, 24 Jan 2020 02:32:37 -0800 Subject: gnu: r-biocset: Fix spelling of "ability". * gnu/packages/bioconductor (r-biocset)[description]: Fix typo. --- gnu/packages/bioconductor.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e2b4f6ea7f..562e151fef 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7349,7 +7349,7 @@ analytics on packages.") (description "BiocSet displays different biological sets in a triple tibble format. These three tibbles are @code{element}, @code{set}, and @code{elementset}. -The user has the abilty to activate one of these three tibbles to perform +The user has the ability to activate one of these three tibbles to perform common functions from the @code{dplyr} package. Mapping functionality and accessing web references for elements/sets are also available in BiocSet.") (license license:artistic2.0))) -- cgit v1.2.3 From fd6412cd2c28c5b0d863428bbfcf998be1b1a4b0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 27 Jan 2020 16:23:38 +0100 Subject: gnu: r-metap: Update to 1.3. * gnu/packages/bioconductor.scm (r-metap): Update to 1.3. --- 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 562e151fef..3fb47884ae 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3165,14 +3165,14 @@ are standardized and usable by the accompanying mutossGUI package.") (define-public r-metap (package (name "r-metap") - (version "1.2") + (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "metap" version)) (sha256 (base32 - "0pfbcixjrzx81l9wqhlp55khg9k63zf8pvg2n39c19akr4ppzhvf")))) + "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) -- cgit v1.2.3 From 062cbc4f2b746f5b7fb1766107b5fd183628ed17 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 27 Jan 2020 20:47:46 +0100 Subject: gnu: r-destiny: Update to 3.0.1. * gnu/packages/bioconductor.scm (r-destiny): Update to 3.0.1. --- 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 3fb47884ae..0b8598a737 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2160,14 +2160,14 @@ possible, parallelization is achieved using the BiocParallel framework.") (define-public r-destiny (package (name "r-destiny") - (version "3.0.0") + (version "3.0.1") (source (origin (method url-fetch) (uri (bioconductor-uri "destiny" version)) (sha256 (base32 - "0vj9nk8g6i4vzm6cnzvbsqcvyk6fhmx0a0nxxrciarffyhqk81yz")))) + "1hzg53p1cz21bvnfyyz40bpvjhg89zi3rahlqf0c4w85iwc1i4vi")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit v1.2.3 From c5d75df36693d677c268b2141fdaa5fb3d767561 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 27 Jan 2020 20:47:57 +0100 Subject: gnu: r-ropls: Update to 1.18.8. * gnu/packages/bioconductor.scm (r-ropls): Update to 1.18.8. --- 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 0b8598a737..b0f224fd5c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5164,14 +5164,14 @@ packages.") (define-public r-ropls (package (name "r-ropls") - (version "1.18.6") + (version "1.18.8") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "1sm2fmygrra9gdcs90lmk5y1ag6arga6159kggx4ij8bkhyc66vb")))) + "033i39r4037nd54jnp5zdn1vpzh61r671vmq0sf8dqrfblhm4w7a")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit v1.2.3 From 0dfaebfa2e90fa044bec102da3704451e57b2d7d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 27 Jan 2020 20:48:04 +0100 Subject: gnu: r-multiassayexperiment: Update to 1.12.2. * gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.12.2. --- 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 b0f224fd5c..469f2897ae 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7177,14 +7177,14 @@ access.") (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") - (version "1.12.1") + (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiAssayExperiment" version)) (sha256 (base32 - "0xpi5qpffg9pn8szkvicpc43a0r534wngyqwvsip8w66zi8c9kpc")))) + "0722f3jl1xq8k8w7vrv986jd16bgysqp3n07pgmdn0hh1zh2mcqc")))) (properties `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) -- cgit v1.2.3 From a38bf7c843c75a6ed55495c75c26ccc7afc44a00 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Mon, 20 Jan 2020 20:21:09 +0100 Subject: gnu: Add r-deconstructsigs. * gnu/packages/bioconductor.scm (r-deconstructsigs): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 469f2897ae..c1da8ac106 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -694,6 +694,34 @@ annotations.") "This is a manifest package for Illumina's EPIC methylation arrays.") (license license:artistic2.0))) +;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19 +;; from Bioconductor. +(define-public r-deconstructsigs + (package + (name "r-deconstructsigs") + (version "1.8.0") + (source (origin + (method url-fetch) + (uri (cran-uri "deconstructSigs" version)) + (sha256 + (base32 + "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a")))) + (properties + `((upstream-name . "deconstructSigs"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bsgenome" ,r-bsgenome) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-reshape2" ,r-reshape2))) + (home-page "https://github.com/raerose01/deconstructSigs") + (synopsis "Identifies signatures present in a tumor sample") + (description "This package takes sample information in the form of the +fraction of mutations in each of 96 trinucleotide contexts and identifies +the weighted combination of published signatures that, when summed, most +closely reconstructs the mutational profile.") + (license license:gpl2+))) + (define-public r-do-db (package (name "r-do-db") -- cgit v1.2.3