that accept short and long options.")
(license license:gpl2+)))
-(define-public r-wgcna
- (package
- (name "r-wgcna")
- (version "1.69")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "WGCNA" version))
- (sha256
- (base32
- "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
- (properties `((upstream-name . "WGCNA")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-doparallel" ,r-doparallel)
- ("r-dynamictreecut" ,r-dynamictreecut)
- ("r-fastcluster" ,r-fastcluster)
- ("r-foreach" ,r-foreach)
- ("r-go-db" ,r-go-db)
- ("r-hmisc" ,r-hmisc)
- ("r-impute" ,r-impute)
- ("r-rcpp" ,r-rcpp)
- ("r-survival" ,r-survival)
- ("r-matrixstats" ,r-matrixstats)
- ("r-preprocesscore" ,r-preprocesscore)))
- (home-page
- "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
- (synopsis "Weighted correlation network analysis")
- (description
- "This package provides functions necessary to perform Weighted
-Correlation Network Analysis on high-dimensional data. It includes functions
-for rudimentary data cleaning, construction and summarization of correlation
-networks, module identification and functions for relating both variables and
-modules to sample traits. It also includes a number of utility functions for
-data manipulation and visualization.")
- (license license:gpl2+)))
-
(define-public r-kernlab
(package
(name "r-kernlab")
;; Either version
(license (list license:gpl2 license:gpl3))))
-(define-public r-fourcseq
- (package
- (name "r-fourcseq")
- (version "1.22.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "FourCSeq" version))
- (sha256
- (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b"))))
- (properties `((upstream-name . "FourCSeq")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biostrings" ,r-biostrings)
- ("r-deseq2" ,r-deseq2)
- ("r-fda" ,r-fda)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggbio" ,r-ggbio)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gtools" ,r-gtools)
- ("r-lsd" ,r-lsd)
- ("r-matrix" ,r-matrix)
- ("r-reshape2" ,r-reshape2)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page
- "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
- (synopsis "Analysis of multiplexed 4C sequencing data")
- (description
- "This package is an R package dedicated to the analysis of (multiplexed)
-4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
-interactions between DNA elements and identify differential interactions
-between conditions. The statistical analysis in R starts with individual bam
-files for each sample as inputs. To obtain these files, the package contains
-a Python script to demultiplex libraries and trim off primer sequences. With
-a standard alignment software the required bam files can be then be
-generated.")
- (license license:gpl3+)))
-
(define-public r-phylogram
(package
(name "r-phylogram")
(define-public r-seurat
(package
(name "r-seurat")
- (version "3.2.0")
+ (version "3.2.1")
(source (origin
(method url-fetch)
(uri (cran-uri "Seurat" version))
(sha256
(base32
- "1vj3dlsqakgnn4x1jz9fkl2cy0jzc5s65h1c20fnamr7lk45pnf2"))))
+ "0jipc4xpmx56jzc31w6nsl77ah8x8wq7jclg2mxhjql4ixkwmz54"))))
(properties `((upstream-name . "Seurat")))
(build-system r-build-system)
(propagated-inputs
- `(("r-ape" ,r-ape)
- ("r-cluster" ,r-cluster)
+ `(("r-cluster" ,r-cluster)
("r-cowplot" ,r-cowplot)
("r-fitdistrplus" ,r-fitdistrplus)
("r-future" ,r-future)
("r-lmtest" ,r-lmtest)
("r-mass" ,r-mass)
("r-matrix" ,r-matrix)
+ ("r-matrixstats" ,r-matrixstats)
("r-miniui" ,r-miniui)
("r-patchwork" ,r-patchwork)
("r-pbapply" ,r-pbapply)
(define-public r-diversitree
(package
(name "r-diversitree")
- (version "0.9-13")
+ (version "0.9-14")
(source
(origin
(method url-fetch)
(uri (cran-uri "diversitree" version))
(sha256
(base32
- "00vi4klywi35hd170ksjv3xja3hqqbkcidcnrrlpgv4179k0azix"))))
+ "0xkxw4n1rsagip51smh9k0h0lmnnvsajqcxma7yh95ifdkyrcyy4"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))