summaryrefslogtreecommitdiff
path: root/gnu/packages/bioconductor.scm
diff options
context:
space:
mode:
Diffstat (limited to 'gnu/packages/bioconductor.scm')
-rw-r--r--gnu/packages/bioconductor.scm345
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
generated by cgit v1.2.3 (git 2.46.0) at 2024-08-27 22:48:40 +0000