From 85d0bd53403fae0c893339a784ac26e945f28656 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 28 May 2019 23:56:27 +0200 Subject: gnu: r-chippeakanno: Update to 3.18.1. * gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.18.1. --- 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 3810749f83..2febfcd9ac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1153,14 +1153,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.18.0") + (version "3.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "089v16mm5m0rlyyyd0d6rz8gwb852zf3bcdrrw70wanlfjn258q7")))) + "1mwi5s600c3jxy8f1azfrndc3g06qvhbmrp9wqac9nwjbfx1kfji")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 13b49976b79858e99efaf65281fd3d9e3304022e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 28 May 2019 23:56:31 +0200 Subject: gnu: r-icobra: Update to 1.12.1. * gnu/packages/bioconductor.scm (r-icobra): 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 2febfcd9ac..b13744eadd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2086,14 +2086,14 @@ independent of the p-value under the null hypothesis.") (define-public r-icobra (package (name "r-icobra") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "1w9frnczgypzc2czbwrvlizqcqhbp6cdpyws7vkmnn9k0ggzxvfc")))) + "1wj0vqyb6h4rddmn4va3182yap9bv4m1r1jlzyjfyrqxhl2sqb1q")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From e4519ee73dfc08e72977d0788807d6150bff66c6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 28 May 2019 23:56:36 +0200 Subject: gnu: r-atacseqqc: Update to 1.8.1. * gnu/packages/bioconductor.scm (r-atacseqqc): 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 b13744eadd..e60f8cac0a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3408,14 +3408,14 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "03f130vcd6hd3fv2pg60id0ddd6qkwsyx73gm907xaayf42ar2pj")))) + "0h5j3724hnd86w22vy3whqx6gkf0nf2dxd2clgzdvjzblbcd5s69")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From d1ee1540d4963e49861c60241596c5529c4d91a4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 30 May 2019 13:40:48 +0200 Subject: gnu: r-dose: Update to 3.10.1. * gnu/packages/bioconductor.scm (r-dose): Update to 3.10.1. --- 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 e60f8cac0a..1e38d796a9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2886,14 +2886,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.10.0") + (version "3.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "0dvhnfhzhhzcxm8zhdwrkif7sak4p888sjqfd3a0p77h0hs6g8pv")))) + "0ab7mgj42fg6608qkciyqivr1n8s8r5ibvp0z3jfclrnyx6cl0w1")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 81e3de01ae2ac0e9cedc5625d25fd9b3d31e07fa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 31 May 2019 14:40:20 +0200 Subject: gnu: Add r-birewire. * gnu/packages/bioconductor.scm (r-birewire): New variable. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e38d796a9..10a4079fea 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4548,3 +4548,32 @@ high-throughput sequencing data. It performs parallel processing of entire files and produces a report which contains a set of high-resolution graphics.") (license license:gpl2+))) + +(define-public r-birewire + (package + (name "r-birewire") + (version "3.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiRewire" version)) + (sha256 + (base32 + "1gjb18l3gq3w8zl6r5d49hw0r1kfh9f7ghv9hz6y86aniprvb518")))) + (properties `((upstream-name . "BiRewire"))) + (build-system r-build-system) + (propagated-inputs + `(("r-igraph" ,r-igraph) + ("r-matrix" ,r-matrix) + ("r-slam" ,r-slam) + ("r-tsne" ,r-tsne))) + (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html") + (synopsis "Tools for randomization of bipartite graphs") + (description + "This package provides functions for bipartite network rewiring through N +consecutive switching steps and for the computation of the minimal number of +switching steps to be performed in order to maximise the dissimilarity with +respect to the original network. It includes functions for the analysis of +the introduced randomness across the switching steps and several other +routines to analyse the resulting networks and their natural projections.") + (license license:gpl3))) -- cgit 1.4.1 From 1a24f855c8dcb61f34b1ec7390ca90e2540c53d9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 31 May 2019 14:40:29 +0200 Subject: gnu: Add r-birta. * gnu/packages/bioconductor.scm (r-birta): New variable. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 10a4079fea..5ffb7c4e3c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4577,3 +4577,32 @@ respect to the original network. It includes functions for the analysis of the introduced randomness across the switching steps and several other routines to analyse the resulting networks and their natural projections.") (license license:gpl3))) + +(define-public r-birta + (package + (name "r-birta") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "birta" version)) + (sha256 + (base32 + "12xjyvgmh4h0b7hi4qg50kcpb9003gnh2xyfgncb8l9mzvsbkxc2")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-limma" ,r-limma) + ("r-mass" ,r-mass))) + (home-page "https://bioconductor.org/packages/birta") + (synopsis "Bayesian inference of regulation of transcriptional activity") + (description + "Expression levels of mRNA molecules are regulated by different +processes, comprising inhibition or activation by transcription factors and +post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian +Inference of Regulation of Transcriptional Activity) uses the regulatory +networks of transcription factors and miRNAs together with mRNA and miRNA +expression data to predict switches in regulatory activity between two +conditions. A Bayesian network is used to model the regulatory structure and +Markov-Chain-Monte-Carlo is applied to sample the activity states.") + (license license:gpl2+))) -- cgit 1.4.1