(define-public r-genomicinteractions
(package
(name "r-genomicinteractions")
- (version "1.20.1")
+ (version "1.20.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GenomicInteractions" version))
(sha256
(base32
- "140bp7c8p079xh5wwxmrq3a73pm6mdc9czq5w2gzjml7dgrca38a"))))
+ "0mqb899wah5n7bp2lajhwy2zpqqhi18plza3i3m51rfl9n62smph"))))
(properties
`((upstream-name . "GenomicInteractions")))
(build-system r-build-system)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)
("r-stringr" ,r-stringr)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
(synopsis "R package for handling genomic interaction data")
(description
("r-singlecellexperiment" ,r-singlecellexperiment)
("r-stringr" ,r-stringr)
("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/RGLab/MAST/")
(synopsis "Model-based analysis of single cell transcriptomics")
(description
(define-public r-gosemsim
(package
(name "r-gosemsim")
- (version "2.12.0")
+ (version "2.12.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GOSemSim" version))
(sha256
(base32
- "0pqnlgdvh5szjhwc1mw1snjgpj9lrsnk44bn164cl3zwvdayccya"))))
+ "1r8yx6qw6d6602cp8aspzl3shi1l1zqcrc8fm9d5wg01sw1whs05"))))
(properties `((upstream-name . "GOSemSim")))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-go-db" ,r-go-db)
("r-rcpp" ,r-rcpp)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://guangchuangyu.github.io/software/GOSemSim")
(synopsis "GO-terms semantic similarity measures")
(description
(define-public r-gofuncr
(package
(name "r-gofuncr")
- (version "1.6.0")
+ (version "1.6.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GOfuncR" version))
(sha256
(base32
- "0hmi13pz923fm95asys615rih63b1i2nvynfczr1zcsc9fzn4h35"))))
+ "1wk7ja6f5il8jx8v05ijzcs9pijp3b953h566ya66xp7dz5jg9rb"))))
(properties `((upstream-name . "GOfuncR")))
(build-system r-build-system)
(propagated-inputs
("r-mapplots" ,r-mapplots)
("r-rcpp" ,r-rcpp)
("r-vioplot" ,r-vioplot)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/GOfuncR/")
(synopsis "Gene ontology enrichment using FUNC")
(description
(define-public r-biosigner
(package
(name "r-biosigner")
- (version "1.14.0")
+ (version "1.14.4")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biosigner" version))
(sha256
(base32
- "1kdfhw629qczrfms0jmphqz0ksjzi8js00xj92h1lnv092npfk0j"))))
+ "0hypk784xcax99mp673md6kvx45chk2nxbqniww7zm9q2hj983hl"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-randomforest" ,r-randomforest)
("r-ropls" ,r-ropls)))
(native-inputs
- `(("r-knitr" ,r-knitr)
- ("r-rmarkdown" ,r-rmarkdown)
- ("pandoc" ,ghc-pandoc)
- ("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes
+ `(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/biosigner/")
(synopsis "Signature discovery from omics data")
(description
(define-public r-cytoml
(package
(name "r-cytoml")
- (version "1.12.0")
+ (version "1.12.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "CytoML" version))
(sha256
(base32
- "0m8x18wkvis85cawv7j07pk59w76wnzy93ia99gd24j82z4h97p1"))))
+ "0wgi8rwb4spxzd5xvs5amfr5g82ny2nad57j3nmhnhnj1cpirjxz"))))
(properties `((upstream-name . "CytoML")))
(build-system r-build-system)
(inputs
("r-runit" ,r-runit)
("r-xml" ,r-xml)
("r-yaml" ,r-yaml)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/RGLab/CytoML")
(synopsis "GatingML interface for cross platform cytometry data sharing")
(description
(define-public r-mixomics
(package
(name "r-mixomics")
- (version "6.10.8")
+ (version "6.10.9")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mixOmics" version))
(sha256
(base32
- "0307vhx9ck24rxqbvq15815ssxcc226sl2la060n204b51wi9jaa"))))
+ "0b457yg8mwqlrn5l344w8qcj8v2ghlj1wdx1ysxbncqvqx7nvgig"))))
(properties `((upstream-name . "mixOmics")))
(build-system r-build-system)
(propagated-inputs
("r-rcolorbrewer" ,r-rcolorbrewer)
("r-reshape2" ,r-reshape2)
("r-tidyr" ,r-tidyr)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "http://www.mixOmics.org")
(synopsis "Multivariate methods for exploration of biological datasets")
(description
(define-public r-bigpint
(package
(name "r-bigpint")
- (version "1.2.0")
+ (version "1.2.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bigPint" version))
(sha256
(base32
- "10vs0lzfyxp6sm4r9pxfwipjvzmmaqnvwn1hc5q37s5qz44fg0hk"))))
+ "1zkakxi1iqavzmjxnkkd02qm5jk28ldcvcdcxaafz748dz6s67fs"))))
(properties `((upstream-name . "bigPint")))
(build-system r-build-system)
(propagated-inputs
("r-shinydashboard" ,r-shinydashboard)
("r-stringr" ,r-stringr)
("r-tidyr" ,r-tidyr)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/lindsayrutter/bigPint")
(synopsis "Big multivariate data plotted interactively")
(description
(define-public r-multiassayexperiment
(package
(name "r-multiassayexperiment")
- (version "1.12.4")
+ (version "1.12.6")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MultiAssayExperiment" version))
(sha256
(base32
- "01cnp00y5bk551c8gqgqp5468dvccg72i0rvh5cxgbx1c42zy6xn"))))
+ "174vzlxsyayb5il77cb3zzgszxl3l0wkprc9w6pgz4yv5ix13adi"))))
(properties
`((upstream-name . "MultiAssayExperiment")))
(build-system r-build-system)
("r-s4vectors" ,r-s4vectors)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-tidyr" ,r-tidyr)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://waldronlab.io/MultiAssayExperiment/")
(synopsis "Integration of multi-omics experiments in Bioconductor")
(description
(define-public r-biocpkgtools
(package
(name "r-biocpkgtools")
- (version "1.4.0")
+ (version "1.4.6")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocPkgTools" version))
(sha256
(base32
- "0gyhb3071pxmvaxla7cxy9k97s3z3ynl62jnqz9jnkd53c7jnd53"))))
+ "0grwnmncmpqcplbfw3j210m1a8f7mmdizklh4zksg4ic21dpjj1a"))))
(properties `((upstream-name . "BiocPkgTools")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocmanager" ,r-biocmanager)
+ `(("r-biocfilecache" ,r-biocfilecache)
+ ("r-biocmanager" ,r-biocmanager)
("r-biocviews" ,r-biocviews)
("r-dplyr" ,r-dplyr)
("r-dt" ,r-dt)
("r-igraph" ,r-igraph)
("r-jsonlite" ,r-jsonlite)
("r-magrittr" ,r-magrittr)
+ ("r-rappdirs" ,r-rappdirs)
("r-rbgl" ,r-rbgl)
("r-readr" ,r-readr)
("r-rex" ,r-rex)
+ ("r-rlang" ,r-rlang)
("r-rvest" ,r-rvest)
("r-stringr" ,r-stringr)
("r-tibble" ,r-tibble)
("r-tidyr" ,r-tidyr)
+ ("r-tidyselect" ,r-tidyselect)
("r-xml2" ,r-xml2)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://github.com/seandavi/BiocPkgTools")
(synopsis "Collection of tools for learning about Bioconductor packages")
(description
(define-public r-biocworkflowtools
(package
(name "r-biocworkflowtools")
- (version "1.12.0")
+ (version "1.12.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocWorkflowTools" version))
(sha256
(base32
- "1v4bhnpdkmllm7aghms9b7369hkrgz7mn69wbrqg1x42pgkf30ad"))))
+ "0z28s572wg9qxv52dmixxz1xf1z3fyp2j7kzk0k32fp628918wr6"))))
(properties
`((upstream-name . "BiocWorkflowTools")))
(build-system r-build-system)
("r-rstudioapi" ,r-rstudioapi)
("r-stringr" ,r-stringr)
("r-usethis" ,r-usethis)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
(synopsis "Tools to aid the development of Bioconductor Workflow packages")
(description