diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 97 |
1 files changed, 93 insertions, 4 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7b0405427c..89547be66d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org> ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -832,6 +833,36 @@ Disease Ontology.") 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 @@ -3453,14 +3484,14 @@ profiles (GO and KEGG) of gene and gene clusters.") (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 @@ -4537,14 +4568,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (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) @@ -6048,3 +6079,61 @@ attributable to individual, tissue, time point, or technical variables. The 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))) + +(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 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+))) |