diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 163 |
1 files changed, 134 insertions, 29 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 171736064c..599704bd9f 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 <rekado@elephly.net> +;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org> ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> @@ -1185,13 +1185,13 @@ of Bioconductor.") (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) @@ -2048,13 +2048,13 @@ high-throughput sequencing experiments.") (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) @@ -2395,17 +2395,51 @@ purposes. The package also contains legacy support for early single-end, 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") - (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 @@ -3247,16 +3281,16 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (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) @@ -3979,14 +4013,14 @@ independent of the p-value under the null hypothesis.") (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 @@ -7528,18 +7562,19 @@ self-organizing map clustering and minimal spanning trees.") (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) @@ -7767,7 +7802,7 @@ accessibility data.") (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.") @@ -8401,14 +8436,14 @@ data.") (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) @@ -8866,14 +8901,14 @@ structures.") (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 @@ -9168,14 +9203,14 @@ also known as views, in a controlled vocabulary.") (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 @@ -9338,14 +9373,14 @@ gene selection, testing relationships, and so on.") (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 @@ -10329,14 +10364,14 @@ quality control.") (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) @@ -10550,7 +10585,7 @@ experiments, and visualize de influence of the involved factors.") "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 @@ -10563,14 +10598,14 @@ relevant, and the minimum expression of the most abundant condition.") (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 @@ -10996,6 +11031,44 @@ optionally include the physical locations or genetic map distances of each SNP 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") @@ -11095,6 +11168,38 @@ export to genome browser viewable files, and functions for enrichment 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") |