diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 52 |
1 files changed, 30 insertions, 22 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0e9e6b13fd..3e93d94651 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6083,19 +6083,20 @@ information as possible.") (define-public r-vegan (package (name "r-vegan") - (version "2.4-6") + (version "2.5-1") (source (origin (method url-fetch) (uri (cran-uri "vegan" version)) (sha256 (base32 - "175mqr42mmxy98gpf3rky8alnkw3w1k90ggdw3cispl36841p76w")))) + "0pynr02d1xngda6c3va8fc4nxpgfkawhzcnz1ws4dnarp9b1w90r")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (propagated-inputs `(("r-cluster" ,r-cluster) + ("r-knitr" ,r-knitr) ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-mgcv" ,r-mgcv) @@ -6251,14 +6252,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.24.3") + (version "1.24.4") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "0xip73hlbr3zry9d7ly9vvvsbb3xjcmfa09lr9fdy528dwjrf084")))) + "1a80yv742fx5c7qav7imsdybphf0d5bixsqyf8w5zng7fk8j16d5")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -7589,13 +7590,13 @@ samples.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.14.1") + (version "1.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "033p6fw46sn7w2yyn14nb9qcnkf30cl0nv6zh014ixflm3iifz39")))) + "1659nj1xps7vliy5955i51x6hvrf16n1z0dfh10mmpaaswn2d2mv")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -9637,13 +9638,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-seurat (package (name "r-seurat") - (version "2.2.1") + (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "1sr82nf38hq07avrfn8vlrzjq7dfm4pcr8l1nh6mnglcql2bk9z2")) + "0kp3lw1s896zkjd6x2wp8qcg7wnm5b40g8vihps13f1m7j4nx7r0")) ;; Delete pre-built jar. (snippet '(begin (delete-file "inst/java/ModularityOptimizer.jar") @@ -9673,11 +9674,15 @@ Main-Class: ModularityOptimizer\n"))) (propagated-inputs `(("r-ape" ,r-ape) ("r-caret" ,r-caret) + ("r-cluster" ,r-cluster) ("r-cowplot" ,r-cowplot) ("r-diffusionmap" ,r-diffusionmap) + ("r-dosnow" ,r-dosnow) ("r-dplyr" ,r-dplyr) ("r-dtw" ,r-dtw) + ("r-fitdistrplus" ,r-fitdistrplus) ("r-fnn" ,r-fnn) + ("r-foreach" ,r-foreach) ("r-fpc" ,r-fpc) ("r-gdata" ,r-gdata) ("r-ggplot2" ,r-ggplot2) @@ -9689,13 +9694,16 @@ Main-Class: ModularityOptimizer\n"))) ("r-igraph" ,r-igraph) ("r-irlba" ,r-irlba) ("r-lars" ,r-lars) + ("r-lmtest" ,r-lmtest) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-metap" ,r-metap) ("r-mixtools" ,r-mixtools) ("r-pbapply" ,r-pbapply) ("r-plotly" ,r-plotly) + ("r-png" ,r-png) ("r-ranger" ,r-ranger) + ("r-rann" ,r-rann) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen) @@ -10170,14 +10178,14 @@ effort and encourages consistency.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.26.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "1bqxfqy0hff87ax92z4lfbjz01ndrz7x8pzm6dlkdmi52p30krm9")))) + "1xlmlngn27iwnr21s9di4059kav1a7c1sajx08wja8yn8f7j06hp")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10222,14 +10230,14 @@ interval to data view, mismatch pileup, and several splicing summaries.") (define-public r-gprofiler (package (name "r-gprofiler") - (version "0.6.4") + (version "0.6.6") (source (origin (method url-fetch) (uri (cran-uri "gProfileR" version)) (sha256 (base32 - "1cka02zbz1rbppm782qpxk1xn9qxbrv2gp5rgf970j906hxm2y0b")))) + "1n6cj12j102b4x9vhyl4dljp1i0r43p23cnhqbx4als2xfxdlqgi")))) (properties `((upstream-name . "gProfileR"))) (build-system r-build-system) (propagated-inputs @@ -10340,14 +10348,14 @@ several related annotation packages.") (define-public r-erma (package (name "r-erma") - (version "0.10.0") + (version "0.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "0gcfs9g8vvdv5vmq9b21kd8sq5mizjj49nfzd4in9zvp4b9v7x1g")))) + "1fi8nc6fbd7i4p9i9hli31xplmdpsxqcdrb8v3nf8fx9klllbdav")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10376,14 +10384,14 @@ by Ernst and Kellis.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "18nfsixh6d2wfrb9laqsgly5w1frzihhak683k0p8fdf51h4aqba")))) + "1q8dz8wcq1r7kr635s9q21g36sxkdybk8khhpa4p57qv8r0gppl0")))) (build-system r-build-system) (propagated-inputs `(("r-erma" ,r-erma) @@ -10593,13 +10601,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.22.0") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "0288xa1jy6nzvz2ha07csmp6dirjw5r7p9vy69q2wsbyzr02ymkp")))) + "0da1jw9my2n2gihs31zyn14wwr23d8v2vij39ll7rm6fma3ydfbl")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs @@ -10841,14 +10849,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.6.8") + (version "1.6.9") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "07wniyrh2fhhkz28v0bfgpvpi1hkkn2cvhacrvvvck142j79944x")))) + "0cs64cnf0xjcgmawr210y99j3gxs6aqgh8081n9827kkqnx2y5dm")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -12814,7 +12822,7 @@ expression report comparing samples in an easily configurable manner.") (define-public pigx-chipseq (package (name "pigx-chipseq") - (version "0.0.10") + (version "0.0.15") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/" @@ -12822,7 +12830,7 @@ expression report comparing samples in an easily configurable manner.") "/pigx_chipseq-" version ".tar.gz")) (sha256 (base32 - "13w99bkr0w4j28ms0yzpl1x6fkpdqay0vh495q3x20bcilsjwnf1")))) + "11v9v3vyda0sv4cl45nki7mm4v4bjfcdq7a70kcvi9h465nq66wg")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; parts of the tests rely on access to the network |