From 40be965e28062ab37ab7c7ed6647600fa8671ed0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 14 Oct 2019 17:58:20 +0200 Subject: gnu: Add r-phastcons100way-ucsc-hg19. * gnu/packages/bioconductor.scm (r-phastcons100way-ucsc-hg19): New variable. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7b0405427c..bb28493935 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -832,6 +832,36 @@ (define-public r-pfam-db using data from public repositories.") (license license:artistic2.0))) +(define-public r-phastcons100way-ucsc-hg19 + (package + (name "r-phastcons100way-ucsc-hg19") + (version "3.7.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "phastCons100way.UCSC.hg19" + version 'annotation)) + (sha256 + (base32 + "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa")))) + (properties + `((upstream-name . "phastCons100way.UCSC.hg19"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bsgenome" ,r-bsgenome) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-genomicscores" ,r-genomicscores) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19") + (synopsis "UCSC phastCons conservation scores for hg19") + (description + "This package provides UCSC phastCons conservation scores for the human +genome (hg19) calculated from multiple alignments with other 99 vertebrate +species.") + (license license:artistic2.0))) + ;;; Experiment data -- cgit v1.2.3 From 16e2e4f27b4d6c3d58b9ba029c923994cdf9c140 Mon Sep 17 00:00:00 2001 From: zimoun Date: Tue, 8 Oct 2019 19:35:16 +0200 Subject: gnu: Add r-htqpcr. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/bioconductor.scm (r-htqpcr): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bb28493935..dc06bcb52d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018 Roel Janssen ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice +;;; Copyright © 2019 Simon Tournier ;;; ;;; This file is part of GNU Guix. ;;; @@ -6078,3 +6079,36 @@ (define-public r-variancepartition package includes dream differential expression analysis for repeated measures.") (license license:gpl2+))) + +(define-public r-htqpcr + (package + (name "r-htqpcr") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "HTqPCR" version)) + (sha256 + (base32 + "09xgj797f0qsbm4jswxw7ijjwa4jxg06bfkq66xfhbvascyyrhg7")))) + (properties `((upstream-name . "HTqPCR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-biobase" ,r-biobase) + ("r-gplots" ,r-gplots) + ("r-limma" ,r-limma) + ("r-rcolorbrewer" ,r-rcolorbrewer))) + (home-page "http://www.ebi.ac.uk/bertone/software") + (synopsis "Automated analysis of high-throughput qPCR data") + (description + "Analysis of Ct values from high throughput quantitative real-time +PCR (qPCR) assays across multiple conditions or replicates. The input data +can be from spatially-defined formats such ABI TaqMan Low Density Arrays or +OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad +Laboratories; conventional 96- or 384-well plates; or microfluidic devices +such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data +loading, quality assessment, normalization, visualization and parametric or +non-parametric testing for statistical significance in Ct values between +features (e.g. genes, microRNAs).") + (license license:artistic2.0))) -- cgit v1.2.3 From 86fb2c63bede56b164cf187ce36700fc8f48d41b Mon Sep 17 00:00:00 2001 From: zimoun Date: Tue, 8 Oct 2019 19:35:18 +0200 Subject: gnu: Add r-unifiedwmwqpcr. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/bioconductor.scm (r-unifiedwmwqpcr): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index dc06bcb52d..2187572117 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6112,3 +6112,28 @@ (define-public r-htqpcr non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs).") (license license:artistic2.0))) + +(define-public r-unifiedwmwqpcr + (package + (name "r-unifiedwmwqpcr") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "unifiedWMWqPCR" version)) + (sha256 + (base32 + "10j70bp5y1x2prz2iagqmwf04y79yqinq08wz4ilh8wggb9f7l8a")))) + (properties + `((upstream-name . "unifiedWMWqPCR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-htqpcr" ,r-htqpcr))) + (home-page "https://bioconductor.org/packages/unifiedWMWqPCR") + (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data") + (description + "This packages implements the unified Wilcoxon-Mann-Whitney Test for qPCR +data. This modified test allows for testing differential expression in qPCR +data.") + (license license:gpl2+))) -- cgit v1.2.3 From b9f39ac986a8e655b384efafaf14ccb5aa9bc45c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 18 Oct 2019 19:23:44 +0200 Subject: gnu: r-mlinterfaces: Update to 1.64.1. * gnu/packages/bioconductor.scm (r-mlinterfaces): Update to 1.64.1. --- 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 2187572117..cf5097a74e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3484,14 +3484,14 @@ (define-public r-clusterprofiler (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.64.0") + (version "1.64.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "0zqvxmvbkig3cc4r5k405s53d7y5ccvrf8kf5j6v8s1kkrklai4j")))) + "1c1hciwy37zpr5bzdjj2xxx2r4jdfmr5w0zmg010lm2985z41gqh")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From ca2b1dcfcd73931358dcd1f9bf79d717044e80a8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 19 Oct 2019 17:29:59 +0200 Subject: gnu: r-xcms: Update to 3.6.2. * gnu/packages/bioconductor.scm (r-xcms): Update to 3.6.2. --- 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 cf5097a74e..6467fecb8c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4568,14 +4568,14 @@ (define-public r-massspecwavelet (define-public r-xcms (package (name "r-xcms") - (version "3.6.1") + (version "3.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "06vhqvvzlkc5bslswagrapmn5ag3x84xg9gxk0fhlmgwapqwki1g")))) + "0icww3f1kahyk96mc07yhsbyiranzm2614n509as09jf8bdhq23v")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit v1.2.3 From b5b0ee3bd0c67510aed218b22117309a486cd4d0 Mon Sep 17 00:00:00 2001 From: Vagrant Cascadian Date: Mon, 11 Nov 2019 18:51:25 -0800 Subject: gnu: r-unifiedwmwqpcr: Fix typo in description. * gnu/packages/bioconductor (r-unifiedwmwqpcr)[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 6467fecb8c..89547be66d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6133,7 +6133,7 @@ (define-public r-unifiedwmwqpcr (home-page "https://bioconductor.org/packages/unifiedWMWqPCR") (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data") (description - "This packages implements the unified Wilcoxon-Mann-Whitney Test for qPCR + "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data.") (license license:gpl2+))) -- cgit v1.2.3