diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 345 |
1 files changed, 289 insertions, 56 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8e13044b1a..7972b6e55c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -118,6 +118,28 @@ analysis.") based on mapping using Entrez Gene identifiers.") (license license:artistic2.0))) +(define-public r-org-sc-sgd-db + (package + (name "r-org-sc-sgd-db") + (version "3.17.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "org.Sc.sgd.db" version + 'annotation)) + (sha256 + (base32 "1anxk5sgzgkdk4n1c7gjyzy56wa2bkifghs9m1mh82l95kyvk2ig")))) + (properties `((upstream-name . "org.Sc.sgd.db"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi)) + (home-page "https://bioconductor.org/packages/org.Sc.sgd.db") + (synopsis "Genome wide annotation for Yeast") + (description + "This package provides genome wide annotation for Yeast, primarily based +on mapping using ORF identifiers from @acronym{SGD, Saccharomyces Genome +Database}.") + (license license:artistic2.0))) + (define-public r-pd-mapping50k-xba240 (package (name "r-pd-mapping50k-xba240") @@ -2863,13 +2885,13 @@ analysis, modelling, and visualization of spike-in controls.") (define-public r-ancombc (package (name "r-ancombc") - (version "2.2.1") + (version "2.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ANCOMBC" version)) (sha256 (base32 - "05gngz6cqihxg4zlf7ymw93qj61a1i19hgp4fkc0cxnkq0pambrd")))) + "0jws3wqgwc0gnp7smc0lsqfw9jbcik36pl7vz9a8ndgwpp9c8653")))) (properties `((upstream-name . "ANCOMBC"))) (build-system r-build-system) (propagated-inputs @@ -3494,6 +3516,67 @@ Bioconductor microarray data containers @code{(ExpressionSet}, supported.") (license license:lgpl2.0+))) +(define-public r-arraymvout + (package + (name "r-arraymvout") + (version "1.58.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "arrayMvout" version)) + (sha256 + (base32 "1wdqcfa0h070lky4m2h5k4wg8lg7014y0gk95gip5zags29zjwqb")))) + (properties `((upstream-name . "arrayMvout"))) + (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-before 'install 'change-home-dir + (lambda _ + ;; Change from /homeless-shelter to /tmp for write permission. + (setenv "HOME" "/tmp")))))) + (propagated-inputs + (list r-affy + r-affycontam + r-biobase + r-lumi + r-mdqc + r-parody)) + (home-page "https://bioconductor.org/packages/arrayMvout") + (synopsis "Multivariate outlier detection for expression array QA") + (description + "This package supports the application of diverse quality metrics to +AffyBatch instances, summarizing these metrics via PCA, and then performing +parametric outlier detection on the PCs to identify aberrant arrays with a +fixed Type I error rate.") + (license license:artistic2.0))) + +(define-public r-arrayquality + (package + (name "r-arrayquality") + (version "1.78.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "arrayQuality" version)) + (sha256 + (base32 "0lq59y4pi13z4v1i1ah78xlchxy34x1lplsh0n42wlk88rk0rqxd")))) + (properties `((upstream-name . "arrayQuality"))) + (build-system r-build-system) + (propagated-inputs + (list r-gridbase + r-hexbin + r-limma + r-marray + r-rcolorbrewer)) + (home-page "http://arrays.ucsf.edu/") + (synopsis "Assessing array quality on spotted arrays") + (description + "This package provides functions for performing print-run and array level +quality assessment.") + (license license:lgpl2.0+))) + (define-public r-asafe (package (name "r-asafe") @@ -6152,13 +6235,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biomartr (package (name "r-biomartr") - (version "1.0.4") + (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "biomartr" version)) (sha256 (base32 - "0hv4z6ycmn58ha7j7zfmyhvs2i37cm48gcalg19dli2kaw1c4210")))) + "14nw44dkyrfw43dc4zwsnvkrmdhsl131m9w1wa80j3qkbhyaypfl")))) (properties `((upstream-name . "biomartr"))) (build-system r-build-system) (propagated-inputs @@ -7005,14 +7088,14 @@ visualization of Illumina DNA methylation array data.") (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.24.0") + (version "2.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "0rl5ix755055i95y5xfb4zv5gih2gkqwqia1r1b3yx12z5ybvkc6")))) + "1x73lln0rlnypl8iia54srl3wrazs94f8rspmjsaqsxwknkym319")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -7195,13 +7278,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.36.3") + (version "1.36.4") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "04bh4481jcj91xdh11ic4519jczck6zmysbpnpbbhykanp31z4pf")))) + "0wwh72sj894m3awk4g2zmkkwqafdjyxzsr49vnd1fiyz909hw02a")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -7848,14 +7931,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.40.0") + (version "1.40.1") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "1zmsk5w8i3cq0983nx1d24a6awrbq7aj2wrapsnizq9gvrsrhbbb")))) + "13pbw5nlkjwplliv2pdwazv2idfjklvw0ykx5ja8rchvzs5f1vk4")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs @@ -8099,6 +8182,31 @@ experiments.") and visualizaton of alternative splicing events generated by rMATS.") (license license:expat))) +(define-public r-mdqc + (package + (name "r-mdqc") + (version "1.62.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "mdqc" version)) + (sha256 + (base32 "0y35z9sw3h77a5g4ah0fxrk5xh7irdw9z0y2jhh6dp0xxcqh6i0k")))) + (properties `((upstream-name . "mdqc"))) + (build-system r-build-system) + (propagated-inputs + (list r-cluster + r-mass)) + (home-page "https://bioconductor.org/packages/mdqc") + (synopsis "Mahalanobis distance quality control for microarrays") + (description + "MDQC is a multivariate quality assessment method for microarrays based +on quality control (QC) reports. The Mahalanobis distance of an array's +quality attributes is used to measure the similarity of the quality of that +array against the quality of the other arrays. Then, arrays with unusually +high distances can be flagged as potentially low-quality.") + (license license:lgpl2.0+))) + (define-public r-metagenomeseq (package (name "r-metagenomeseq") @@ -10264,13 +10372,13 @@ tools either included in speaq or available elsewhere on CRAN.") (define-public r-spectra (package (name "r-spectra") - (version "1.10.2") + (version "1.10.3") (source (origin (method url-fetch) (uri (bioconductor-uri "Spectra" version)) (sha256 (base32 - "1jrlfm6k6v4vhzl4lg6sa49yw35ds9x3v7iyc2cvbxqmpp5haila")))) + "1fx6xkl29frfk8bzz5jvr1cn0hjyi46ck23izb1cypiag4lsrf8v")))) (properties `((upstream-name . "Spectra"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -10582,24 +10690,25 @@ of gene-level counts.") (define-public r-valr (package (name "r-valr") - (version "0.6.8") + (version "0.7.0") (source (origin (method url-fetch) (uri (cran-uri "valr" version)) (sha256 (base32 - "156sqh474synjvdm1j332ab75rqab0n81d674xbgs3rfxlr2ksgz")))) + "038s5n8cbffpb9132rpw7q82cxfzlsc86fcywhv63c8szm5g9nrk")))) (build-system r-build-system) (propagated-inputs (list r-broom r-cli r-dplyr r-ggplot2 + r-lifecycle r-rcpp r-readr r-rlang - r-rtracklayer ;bioconductor package + r-rtracklayer r-stringr r-tibble)) (native-inputs @@ -11080,32 +11189,57 @@ problems in genomics, brain imaging, astrophysics, and data mining.") @code{Rcpp}.") (license license:gpl2+))) +(define-public r-apcomplex + (package + (name "r-apcomplex") + (version "2.66.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "apComplex" version)) + (sha256 + (base32 "057p1bsqqw3r49bsx78prqc4jha468bfx50gpl62giix0cfs007f")))) + (properties `((upstream-name . "apComplex"))) + (build-system r-build-system) + (propagated-inputs + (list r-graph + r-org-sc-sgd-db + r-rbgl + r-rgraphviz)) + (home-page "https://bioconductor.org/packages/apComplex") + (synopsis "Estimate protein complex membership using AP-MS protein data") + (description + "This package provides functions to estimate a bipartite graph of protein +complex membership using @acronym{AP-MS, affinity purification–mass +spectrometry} data.") + (license license:lgpl2.0+))) + (define-public r-apeglm (package - (name "r-apeglm") - (version "1.22.1") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "apeglm" version)) - (sha256 - (base32 - "19r1mhpkn3xy6l188c14k9xgn25xqc718bwrlmnz63lak6mp4ws7")))) - (properties `((upstream-name . "apeglm"))) - (build-system r-build-system) - (propagated-inputs - (list r-emdbook - r-genomicranges - r-rcpp - r-rcppeigen - r-rcppnumerical - r-summarizedexperiment)) - (native-inputs (list r-knitr r-rmarkdown)) - (home-page "https://bioconductor.org/packages/apeglm") - (synopsis "Approximate posterior estimation for GLM coefficients") - (description "This package provides Bayesian shrinkage estimators for + (name "r-apeglm") + (version "1.22.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "apeglm" version)) + (sha256 + (base32 + "19r1mhpkn3xy6l188c14k9xgn25xqc718bwrlmnz63lak6mp4ws7")))) + (properties `((upstream-name . "apeglm"))) + (build-system r-build-system) + (propagated-inputs + (list r-emdbook + r-genomicranges + r-rcpp + r-rcppeigen + r-rcppnumerical + r-summarizedexperiment)) + (native-inputs (list r-knitr r-rmarkdown)) + (home-page "https://bioconductor.org/packages/apeglm") + (synopsis "Approximate posterior estimation for GLM coefficients") + (description "This package provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.") - (license license:gpl2))) + (license license:gpl2))) (define-public r-greylistchip (package @@ -14197,6 +14331,42 @@ analyzed in parallel the library performs a number of tests to assure that the data set is suitable for such analysis.") (license license:gpl3))) +(define-public r-anota2seq + (package + (name "r-anota2seq") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "anota2seq" version)) + (sha256 + (base32 "0pmk45276bl3qppzxlp4jpc8bsvdpca8nzrdl6c4n9r3xhzfpyq0")))) + (properties `((upstream-name . "anota2seq"))) + (build-system r-build-system) + (propagated-inputs + (list r-deseq2 + r-edger + r-limma + r-multtest + r-qvalue + r-rcolorbrewer + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/anota2seq") + (synopsis "Transcriptome-wide analysis of translational efficiency") + (description + "The anota2seq package provides analysis of translational efficiency and +differential expression analysis for polysome-profiling and ribosome-profiling +studies (two or more sample classes) quantified by RNA sequencing or +DNA-microarray. Polysome-profiling and ribosome-profiling typically generate +data for two RNA sources, translated mRNA and total mRNA. Analysis of +differential expression is used to estimate changes within each RNA source. +Analysis of translational efficiency aims to identify changes in translation +efficiency leading to altered protein levels that are independent of total +mRNA levels or buffering, a mechanism regulating translational efficiency so +that protein levels remain constant despite fluctuating total mRNA levels.") + (license license:gpl3))) + (define-public r-sigpathway (package (name "r-sigpathway") @@ -14355,18 +14525,19 @@ correspondance between different data sources.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.20.1") + (version "1.20.3") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "0yxnh5bmfcfsciwm852rbb707v9zbky3lsz2xsyyaapm5jjb6npk")))) + "11hgxs42wvirv6b9ywr2jb51s67k4r0pm21dkvm7xjbsbarlkhmh")))) (build-system r-build-system) (propagated-inputs (list r-aplot r-dose + r-ggfun r-ggnewscale r-ggplot2 r-ggraph @@ -15439,14 +15610,14 @@ decomposition algorithms.") (define-public r-yapsa (package (name "r-yapsa") - (version "1.25.0") + (version "1.26.8") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 - "0xva7vljq2k78rzjnjlp4x3ylwk86jaqn2cgbff4h4sb8rfdya7c")))) + "16rr2bkni3jx5qskr5fz5lvf23d03xgd3m4068mnd3n9r23hpb4p")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs @@ -18302,14 +18473,14 @@ using whole genome sequencing data.") (define-public r-activepathways (package (name "r-activepathways") - (version "2.0.0") + (version "2.0.2") (source (origin (method url-fetch) (uri (cran-uri "ActivePathways" version)) (sha256 (base32 - "1niwzbzqs1s0mx6ia8fmvg9db6kajs0rdxgnnn1pq68yd8rjn79g")))) + "1h0ih87pf6b5mdhmh65frv3nqx7v5adqv37wn2p3gkpszd6hwc79")))) (properties `((upstream-name . "ActivePathways"))) (build-system r-build-system) @@ -18499,6 +18670,37 @@ the read count and GC content bias.") validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") (license license:artistic2.0))) +(define-public r-hybridmtest + (package + (name "r-hybridmtest") + (version "1.44.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "HybridMTest" version)) + (sha256 + (base32 "19pycad35hc7ylnsz75bv029y1r6j9xvrbhzk4i64i7jn8gi7ngh")))) + (properties `((upstream-name . "HybridMTest"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-fdrtool + r-mass + r-survival)) + (home-page "https://bioconductor.org/packages/HybridMTest") + (synopsis "Hybrid multiple testing") + (description + "This package performs hybrid multiple testing that incorporates method +selection and assumption evaluations into the analysis using @acronym{EBP, +empirical Bayes probability} estimates obtained by Grenander density +estimation. For instance, for 3-group comparison analysis, Hybrid Multiple +testing considers EBPs as weighted EBPs between F-test and H-test with EBPs +from Shapiro Wilk test of normality as weigth. Instead of just using EBPs +from F-test only or using H-test only, this methodology combines both types of +EBPs through EBPs from Shapiro Wilk test of normality. This methodology uses +then the law of total EBPs.") + (license license:gpl2+))) + (define-public r-hypergraph (package (name "r-hypergraph") @@ -18964,13 +19166,13 @@ different graph related packages produced by Bioconductor.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.28.0") + (version "2.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "04npnfmz1p1vpwrdsim309k7518i4p1li04xnmw8c9zgdb6yl61a")))) + "11v3gzy88fai0rhdymvj9k74g7hjc6n9fihfrrnw0qfr447z1d61")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) @@ -19700,13 +19902,13 @@ array-like semantic. It also provides: (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.38.1") + (version "0.38.2") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0qpjx64ilc1niglhf6pn47damgaf5vdzwkvnlhcixqzpl28ndbs9")))) + "0n1w451647pxii6qrrxbvdi9z6rqdwibczkbs7k7a9j33bv3nqv8")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -21001,14 +21203,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.44.1") + (version "1.44.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0yfmpxvx7h344fp6i3iny7r61n904bj0qdy14qbsp3d0z4g8a5fn")))) + "0laismy8kklzkg81r5vf1194fbhp2hw952g6jc3zvn2z5y2d4524")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -21258,6 +21460,27 @@ statistical dependencies in messy, complex data.") other functional sequencing data.") (license license:gpl2))) +(define-public r-parody + (package + (name "r-parody") + (version "1.58.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "parody" version)) + (sha256 + (base32 "0n2pmpnpwh16hb58v821xn42jm4a7wjsdf6sqxapjjw9w432mjac")))) + (properties `((upstream-name . "parody"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/parody") + (synopsis "Parametric and resistant outlier detection") + (description + "The parody package provides routines for univariate and multivariate +outlier detection with a focus on parametric methods, but support for some +methods based on resistant statistics.") + (license license:artistic2.0))) + (define-public r-pathview (package (name "r-pathview") @@ -21853,19 +22076,20 @@ the Bioconductor project.") (define-public r-biodb (package (name "r-biodb") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biodb" version)) (sha256 (base32 - "1lcjq1zfarhc7pqqrkqnaycsv2f27n4n8mfvrc3c9ww4lsza555k")))) + "18j70ma85qb42qqpzz8fw3g4x6cav4j0pc2ab5ym22791dr8izck")))) (properties `((upstream-name . "biodb"))) (build-system r-build-system) (propagated-inputs (list r-biocfilecache r-chk + r-git2r r-jsonlite r-lgr r-lifecycle @@ -21979,6 +22203,15 @@ design.") "0n026b744ah5kcnipsyiqqs7vlz5n5im1kgv35i2pgxyzvf7a8sn")))) (properties `((upstream-name . "biomvRCNS"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'patch-constants + (lambda _ + (substitute* "src/biomvRCNS.c" + (("DOUBLE_XMIN") "DBL_MIN") + (("DOUBLE_XMAX") "DBL_MAX"))))))) (propagated-inputs (list r-genomicranges r-gviz r-iranges r-mvtnorm)) (home-page "https://bioconductor.org/packages/biomvRCNS") @@ -22380,13 +22613,13 @@ interest on transformed methylation proportions.") (define-public r-omnipathr (package (name "r-omnipathr") - (version "3.8.0") + (version "3.8.2") (source (origin (method url-fetch) (uri (bioconductor-uri "OmnipathR" version)) (sha256 - (base32 "0r2nv3nbadnvqby7p5bdpl9fxjb30h0c8kjv1dkqqnhk5rbfl4hf")))) + (base32 "13ac98jj03vkzrc1ghrs98qrfvr74wz099w26lgc7jw2yxj575as")))) (properties `((upstream-name . "OmnipathR"))) (build-system r-build-system) (arguments @@ -22406,13 +22639,13 @@ interest on transformed methylation proportions.") r-later r-logger r-magrittr - r-rmarkdown r-progress r-purrr r-rappdirs r-readr r-readxl r-rlang + r-rmarkdown r-rvest r-stringr r-tibble @@ -22581,14 +22814,14 @@ embeddings and functions to build new reference.") (define-public r-tximeta (package (name "r-tximeta") - (version "1.18.1") + (version "1.18.3") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 - "02240v41scaqxabjb62zh6shkkzb9520dhn0lfc2jbimnb26yj7f")))) + "01s8x8a3rb0a5i599pxc5miz84ssvh10b4vha79nmbhkqccffvml")))) (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs |