From 0e434dad70075f87b80b5899758d0b2c3289c6ff Mon Sep 17 00:00:00 2001 From: Vagrant Cascadian Date: Tue, 20 Apr 2021 14:16:48 -0700 Subject: gnu: r-msmstests: Fix typo. * gnu/packages/bioconductor.scm (r-msmstests)[description]: Fix "This package" 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 171736064c..89bf8f0964 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10550,7 +10550,7 @@ (define-public r-msmstests "https://bioconductor.org/packages/msmsTests") (synopsis "Differential LC-MS/MS expression tests") (description - "This packages provides statistical tests for label-free LC-MS/MS data + "This package provides statistical tests for label-free LC-MS/MS data by spectral counts, to discover differentially expressed proteins between two biological conditions. Three tests are available: Poisson GLM regression, quasi-likelihood GLM regression, and the negative binomial of the edgeR -- cgit v1.2.3 From eb34afe1be30ad884d2a0960d0e4d02c7b106b34 Mon Sep 17 00:00:00 2001 From: Vagrant Cascadian Date: Wed, 21 Apr 2021 08:12:50 -0700 Subject: gnu: r-circrnaprofiler: Fix grammar. * gnu/packages/bioconductor.scm (r-circrnaprofiler)[description]: Remove gratuitous use of "allows to". --- 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 89bf8f0964..c1454f25e8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7767,7 +7767,7 @@ (define-public r-circrnaprofiler (description "@code{r-circrnaprofiler} is a computational framework for a comprehensive in silico analysis of @dfn{circular RNA} (circRNAs). This computational -framework allows to combine and analyze circRNAs previously detected by +framework allows combining and analyzing circRNAs previously detected by multiple publicly available annotation-based circRNA detection tools. It covers different aspects of circRNAs analysis from differential expression analysis, evolutionary conservation, biogenesis to functional analysis.") -- cgit v1.2.3 From aa9a94bba9a5705c6a4bfb19268dc616b7f4f7d3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 07:09:50 +0200 Subject: gnu: r-abn: Update to 2.5-0. * gnu/packages/cran.scm (r-abn): Move from here... * gnu/packages/bioconductor.scm (r-abn): ...to here; update to 2.5-0. [propagated-inputs]: Add r-rgraphviz. --- gnu/packages/bioconductor.scm | 38 ++++++++++++++++++++++++++++++++++++++ gnu/packages/cran.scm | 35 ----------------------------------- 2 files changed, 38 insertions(+), 35 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c1454f25e8..da6650b191 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10996,6 +10996,44 @@ (define-public r-ldheatmap on the plot.") (license license:gpl3))) +;; This is a CRAN package, but it depends on r-rgraphviz, which is a +;; Bioconductor package. +(define-public r-abn + (package + (name "r-abn") + (version "2.5-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "abn" version)) + (sha256 + (base32 + "1fqmhw0mhdl6az1gpg0byvx5snhz1pl3fqikhyfjcjrc9xbsq8yw")))) + (build-system r-build-system) + (inputs + `(("gsl" ,gsl))) + (propagated-inputs + `(("r-lme4" ,r-lme4) + ("r-nnet" ,r-nnet) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-rgraphviz" ,r-rgraphviz) + ("r-rjags" ,r-rjags))) + (home-page "https://r-bayesian-networks.org/") + (synopsis "Modelling multivariate data with additive bayesian networks") + (description + "Bayesian network analysis is a form of probabilistic graphical models +which derives from empirical data a directed acyclic graph, DAG, describing +the dependency structure between random variables. An additive Bayesian +network model consists of a form of a DAG where each node comprises a +@dfn{generalized linear model} (GLM). Additive Bayesian network models are +equivalent to Bayesian multivariate regression using graphical modelling, they +generalises the usual multivariable regression, GLM, to multiple dependent +variables. This package provides routines to help determine optimal Bayesian +network models for a given data set, where these models are used to identify +statistical dependencies in messy, complex data.") + (license license:gpl2+))) + (define-public r-pathview (package (name "r-pathview") diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 35c35e6716..d5b71d65d3 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -8037,41 +8037,6 @@ (define-public r-entropy there are functions for discretizing continuous random variables.") (license license:gpl3+))) -(define-public r-abn - (package - (name "r-abn") - (version "2.3-0") - (source - (origin - (method url-fetch) - (uri (cran-uri "abn" version)) - (sha256 - (base32 - "17vdrqm6qp5aijg00ah2imj3pqr6cl5r43hgg8dijbrbhznarci6")))) - (build-system r-build-system) - (inputs - `(("gsl" ,gsl))) - (propagated-inputs - `(("r-lme4" ,r-lme4) - ("r-nnet" ,r-nnet) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rjags" ,r-rjags))) - (home-page "https://r-bayesian-networks.org/") - (synopsis "Modelling multivariate data with additive bayesian networks") - (description - "Bayesian network analysis is a form of probabilistic graphical models -which derives from empirical data a directed acyclic graph, DAG, describing -the dependency structure between random variables. An additive Bayesian -network model consists of a form of a DAG where each node comprises a -@dfn{generalized linear model} (GLM). Additive Bayesian network models are -equivalent to Bayesian multivariate regression using graphical modelling, they -generalises the usual multivariable regression, GLM, to multiple dependent -variables. This package provides routines to help determine optimal Bayesian -network models for a given data set, where these models are used to identify -statistical dependencies in messy, complex data.") - (license license:gpl2+))) - (define-public r-acd (package (name "r-acd") -- cgit v1.2.3 From 8bd3170bcf1791bcb2e3fdc0620e09af4909f4de Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 09:02:36 +0200 Subject: gnu: r-biocgenerics: Update to 0.36.1. * gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.36.1. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index da6650b191..773c446538 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus +;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen ;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2016 Ben Woodcroft @@ -1185,13 +1185,13 @@ (define-public r-biocversion (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.36.0") + (version "0.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "1y9pgangz2f0n9v3zj8brz8bv7a1yjsncdnd5h1l7zv0c0j9fh9q")))) + "0x8cllriayrs99wd5l003iq6i28rb1mci23qcn13ga85578f5lz5")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) -- cgit v1.2.3 From fc1aef2ccdfcac4608e6501ce18e0e1dddf72aed Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 09:02:42 +0200 Subject: gnu: r-genomeinfodb: Update to 1.26.7. * gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.26.7. --- 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 773c446538..16119b12b5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2048,13 +2048,13 @@ (define-public r-genefilter (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.26.6") + (version "1.26.7") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1wy4dwiv0pgim975var802z565py4a0nakx6zdvbhry4c0dfczd1")))) + "0fp7sp3jmc2a1hk4r624lfavx8gc2ik3lv43ksc2jmspg6cvh516")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) -- cgit v1.2.3 From 390098ddd40b5c7bfdcb22bf057533e97122f8dd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 09:02:51 +0200 Subject: gnu: r-systempiper: Update to 1.24.6. * gnu/packages/bioconductor.scm (r-systempiper): Update to 1.24.6. --- 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 16119b12b5..13e727c8f7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2398,14 +2398,14 @@ (define-public r-shortread (define-public r-systempiper (package (name "r-systempiper") - (version "1.24.3") + (version "1.24.6") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki")))) + "05qnn105gm423fka4kb84vpgzjmz1py6mxpfa2agwwmc5v012qbp")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b2bdc2f1302d59984b24f2869c7efc3ff8c4038f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 09:03:10 +0200 Subject: gnu: r-interactionset: Update to 1.18.1. * gnu/packages/bioconductor.scm (r-interactionset): Update to 1.18.1. --- gnu/packages/bioconductor.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 13e727c8f7..f5b71f4ce7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3247,16 +3247,16 @@ (define-public r-riboseqr (license license:gpl3))) (define-public r-interactionset - (package ;BROKEN + (package (name "r-interactionset") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "14lp23b298wr3r7ggcfvas0xlf1866cpla0rv7dz589f50z6bj31")))) + "0dx6yw6rxgkcidnnyjzv57vzd112nf9n2bj6dkv7r3a2d2wj6xh4")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) -- cgit v1.2.3 From b410f072b547dc5f49ac2370952a02d25c47b5d9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 09:03:17 +0200 Subject: gnu: r-icobra: Update to 1.18.1. * gnu/packages/bioconductor.scm (r-icobra): Update to 1.18.1. --- 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 f5b71f4ce7..8edd4ce339 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3979,14 +3979,14 @@ (define-public r-ihw (define-public r-icobra (package (name "r-icobra") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "0knqvvfi5y53jk8s2g2bqgxnh2pbdf38676fk7pkdp1r2j6cbi3s")))) + "183asczy9v2v1vrzxb7n7pa2yfzym3l24r3737k0jg6hnp2bpw50")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 5bd5f755f2bbaaa819857d80ed549abd3c789cf9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 09:03:25 +0200 Subject: gnu: r-universalmotif: Update to 1.8.5. * gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.8.5. --- 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 8edd4ce339..f10580ea63 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8401,14 +8401,14 @@ (define-public r-unifiedwmwqpcr (define-public r-universalmotif (package (name "r-universalmotif") - (version "1.8.4") + (version "1.8.5") (source (origin (method url-fetch) (uri (bioconductor-uri "universalmotif" version)) (sha256 (base32 - "0pmi5mp5v0srr482vlkfmkp28bywq969fvv9g5kjl5rxki963zmr")))) + "07862bs771xldmdnq0zr8926dr299ach8nrgci14p5bbrc88l3ly")))) (properties `((upstream-name . "universalmotif"))) (build-system r-build-system) -- cgit v1.2.3 From c1942727cfc37a14b732c1903b379250e721f447 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 09:03:38 +0200 Subject: gnu: r-bioassayr: Update to 1.28.3. * gnu/packages/bioconductor.scm (r-bioassayr): Update to 1.28.3. --- 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 f10580ea63..d3e16afc90 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8866,14 +8866,14 @@ (define-public r-chemminer (define-public r-bioassayr (package (name "r-bioassayr") - (version "1.28.2") + (version "1.28.3") (source (origin (method url-fetch) (uri (bioconductor-uri "bioassayR" version)) (sha256 (base32 - "0ylnnm31jkmi8zz78kngqv36yn6i5lvjp1i27v59svw13m4r03g5")))) + "03pdb76j7c28b1h1flb40ahq7i9iha22kblq6mkl3x4xmrdgaw5y")))) (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b75b3ba2c7d03665394c4e68f85a6c843cdef9ae Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 09:03:44 +0200 Subject: gnu: r-experimenthub: Update to 1.16.1. * gnu/packages/bioconductor.scm (r-experimenthub): Update to 1.16.1. --- 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 d3e16afc90..499211ddc7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9168,14 +9168,14 @@ (define-public r-biocviews (define-public r-experimenthub (package (name "r-experimenthub") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHub" version)) (sha256 (base32 - "1zi7vsrhf1hj27rlzrxl4jd81fqh1yhn0svp2d9w71fizsi71akg")))) + "1iyf052hh2dhlwzwwrj571cwr3hd9wp2j915sqg77x6jn40wjr1g")))) (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 3c59d3410766e3c8abe25a7a6389d05ab9e55470 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 09:03:53 +0200 Subject: gnu: r-biocpkgtools: Update to 1.8.2. * gnu/packages/bioconductor.scm (r-biocpkgtools): Update to 1.8.2. --- 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 499211ddc7..9bc372dcae 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9338,14 +9338,14 @@ (define-public r-biocor (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.8.0") + (version "1.8.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "12j4vag40zdgrxfzaqvf3ly7776qyziryz04c3jqzgsqfvzvzz8m")))) + "18m816mh1ic0znp38wax8xppai77lkym3w84x4x30x2mf0vriqfw")))) (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 2191a414ea3088f2f25402e7b344c16f76f70dc9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 09:04:01 +0200 Subject: gnu: r-scran: Update to 1.18.7. * gnu/packages/bioconductor.scm (r-scran): Update to 1.18.7. --- 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 9bc372dcae..206def7082 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10329,14 +10329,14 @@ (define-public r-scater (define-public r-scran (package (name "r-scran") - (version "1.18.5") + (version "1.18.7") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "0mk4bs7pkzbaiaaap75nzsrlwr883h45xnbpn94fy91i8d9w1xy1")))) + "0hsr58b7xj2cqdkyjdpzyifg5wrl1lbylq2h91zbjh5861qjv2n4")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) -- cgit v1.2.3 From 4286233e773d6582378deefb2392e0971aadf100 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 09:04:09 +0200 Subject: gnu: r-catalyst: Update to 1.14.1. * gnu/packages/bioconductor.scm (r-catalyst): 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 206def7082..27fd08daf1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -10563,14 +10563,14 @@ (define-public r-msmstests (define-public r-catalyst (package (name "r-catalyst") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "CATALYST" version)) (sha256 (base32 - "13af7c4irx1f5yqi32k7kj661vzg32wn3dnps7r9pjijfl4drhrh")))) + "04b5kcvkfiw4ina11x3qf5kwrb7056zihm7xp1919bqm8k7nl3mn")))) (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b602ec9fbad8e9ef30a41ed7d6432b0e4aff7516 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 09:04:14 +0200 Subject: gnu: r-mixomics: Update to 6.14.1. * gnu/packages/bioconductor.scm (r-mixomics): Update to 6.14.1. [propagated-inputs]: Add r-biocparallel. --- 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 27fd08daf1..79aaf92124 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7528,18 +7528,19 @@ (define-public r-flowsom (define-public r-mixomics (package (name "r-mixomics") - (version "6.14.0") + (version "6.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "0q43ay5r0qsx0zjjnrq24fk6pq5cimviky5lm4w2mbjclqf0gv0q")))) + "07d1z33bc3bym1jwp1qqfhs18w4v9axk0ycnmldmj6piswvp44wk")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs - `(("r-corpcor" ,r-corpcor) + `(("r-biocparallel" ,r-biocparallel) + ("r-corpcor" ,r-corpcor) ("r-dplyr" ,r-dplyr) ("r-ellipse" ,r-ellipse) ("r-ggrepel" ,r-ggrepel) -- cgit v1.2.3 From 7694acebd18d9b32fd01b70819c1e79de05b4f52 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 10:11:34 +0200 Subject: gnu: r-summarizedexperiment: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Move variable from here... * gnu/packages/bioconductor.scm (r-summarizedexperiment): ...to here. --- gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 34 ---------------------------------- 2 files changed, 34 insertions(+), 34 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 79aaf92124..9b49c6ec43 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2395,6 +2395,40 @@ (define-public r-shortread ungapped alignment formats.") (license license:artistic2.0))) +(define-public r-summarizedexperiment + (package + (name "r-summarizedexperiment") + (version "1.20.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "SummarizedExperiment" version)) + (sha256 + (base32 + "04x6d4mcsnvz6glkmf6k2cv3fs8zk03i9rvv0ahpl793n8l411ps")))) + (properties + `((upstream-name . "SummarizedExperiment"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-delayedarray" ,r-delayedarray) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) + ("r-matrixgenerics" ,r-matrixgenerics) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/SummarizedExperiment") + (synopsis "Container for representing genomic ranges by sample") + (description + "The SummarizedExperiment container contains one or more assays, each +represented by a matrix-like object of numeric or other mode. The rows +typically represent genomic ranges of interest and the columns represent +samples.") + (license license:artistic2.0))) + (define-public r-systempiper (package (name "r-systempiper") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index eda7416fb2..de76e67f57 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7838,40 +7838,6 @@ (define-public bio-vcf (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-summarizedexperiment - (package - (name "r-summarizedexperiment") - (version "1.20.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "SummarizedExperiment" version)) - (sha256 - (base32 - "04x6d4mcsnvz6glkmf6k2cv3fs8zk03i9rvv0ahpl793n8l411ps")))) - (properties - `((upstream-name . "SummarizedExperiment"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/SummarizedExperiment") - (synopsis "Container for representing genomic ranges by sample") - (description - "The SummarizedExperiment container contains one or more assays, each -represented by a matrix-like object of numeric or other mode. The rows -typically represent genomic ranges of interest and the columns represent -samples.") - (license license:artistic2.0))) - (define-public r-genomicalignments (package (name "r-genomicalignments") -- cgit v1.2.3 From bee797fa930e9357dcdf878526e75363f81ac4e7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 4 May 2021 15:37:04 +0200 Subject: gnu: Add r-guitar. * gnu/packages/bioconductor.scm (r-guitar): New variable. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9b49c6ec43..599704bd9f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11168,6 +11168,38 @@ (define-public r-chromstar analyses.") (license license:artistic2.0))) +(define-public r-guitar + (package + (name "r-guitar") + (version "2.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Guitar" version)) + (sha256 + (base32 + "0lvfrpgrvmrz4f4qmsii70hw10h72zh1g1alv2sf6a6ixhndm0mz")))) + (properties `((upstream-name . "Guitar"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-dplyr" ,r-dplyr) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-knitr" ,r-knitr) + ("r-magrittr" ,r-magrittr) + ("r-rtracklayer" ,r-rtracklayer))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/Guitar") + (synopsis "Visualize genomic features") + (description + "This package is designed for visualization of RNA-related genomic +features with respect to the landmarks of RNA transcripts, i.e., transcription +starting site, start codon, stop codon and transcription ending site.") + (license license:gpl2))) + (define-public r-sushi (package (name "r-sushi") -- cgit v1.2.3