diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 89 |
1 files changed, 44 insertions, 45 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ec18568e53..27ece61f2a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1971,13 +1971,13 @@ downloaded from Encode.") (define-public r-hdcytodata (package (name "r-hdcytodata") - (version "1.22.0") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "HDCytoData" version 'experiment)) (sha256 (base32 - "1xqwkwxaaj5yylx9pzvka8pj9gxg1z4g23d2sralcvqzcz7q13zn")))) + "1048xgypsw257ihy0ysfxy5443dzhzp2rkjjvpivvrhw4dzl25ir")))) (properties `((upstream-name . "HDCytoData"))) (build-system r-build-system) (arguments @@ -4529,13 +4529,13 @@ Various visual and textual types of output are available.") (define-public r-bambu (package (name "r-bambu") - (version "3.4.0") + (version "3.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "bambu" version)) (sha256 (base32 - "02pcab8jfwlx4y00yky63anba61bb1h884m0f6ajvasfpgl30w6i")))) + "0j2ivn93dpn7xas0bzfxhwmqzxzscgc3sjkx85y5v2ra1i6jy5k7")))) (properties `((upstream-name . "bambu"))) (build-system r-build-system) (propagated-inputs @@ -6646,14 +6646,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "3.10.0") + (version "3.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "1mx3vip1rx5lq0vnkxpmkyksnq4vygmww85vxq3spr0fah1pwnkr")))) + "12vc573gmg8bwcfa268yq7npg7mivhngx4lx16nzan56rqb475yx")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs @@ -7415,13 +7415,13 @@ exploration of the results.") (define-public r-diffcyt (package (name "r-diffcyt") - (version "1.22.0") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "diffcyt" version)) (sha256 - (base32 "1k3gzzgda29m2v7v8hqw7c2s8z778p0plqxag443lhsxcm6izcxi")))) + (base32 "1lg7c33mdnp35b15n7ydmz4wgkgls6ii3r1q699i4ifxcgxjm8pj")))) (properties `((upstream-name . "diffcyt"))) (build-system r-build-system) (propagated-inputs @@ -7480,13 +7480,13 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-dittoseq (package (name "r-dittoseq") - (version "1.14.2") + (version "1.14.3") (source (origin (method url-fetch) (uri (bioconductor-uri "dittoSeq" version)) (sha256 (base32 - "0qyiq6azknjqim0hjy5xw5gvs5jyczx29vcs95dwsfk92sygdps0")))) + "019fdjjgzh15pbp8m16g73whbjffpm4p7hwk1nz85yc2yr1381zi")))) (properties `((upstream-name . "dittoSeq"))) (build-system r-build-system) (propagated-inputs @@ -8221,13 +8221,13 @@ Enrichment Analysis} (GSEA).") (define-public r-gsva (package (name "r-gsva") - (version "1.50.1") + (version "1.50.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GSVA" version)) (sha256 (base32 - "0ld0bbl6ar3yhi6ncg9d8q60hg4m4v5kphl044fw63l19ixln7cf")))) + "1xgp311wh7ykvnk7nh5xik1kp2b2r08vx595znmzn28fc8rz62b1")))) (properties `((upstream-name . "GSVA"))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -10952,13 +10952,13 @@ single-cell RNA-seq.") (define-public r-seqarray (package (name "r-seqarray") - (version "1.42.2") + (version "1.42.4") (source (origin (method url-fetch) (uri (bioconductor-uri "SeqArray" version)) (sha256 (base32 - "1bwqyvvfwwscznwi1bm4wh2pqf0fmq68g7siwbbw5ypj087ibnnm")))) + "0k7g4wkj1l35pjy6gb3bdlmz5g8q2d596glj09ggm73aaj3z4m9d")))) (properties `((upstream-name . "SeqArray"))) (build-system r-build-system) (propagated-inputs (list r-biostrings @@ -11360,13 +11360,13 @@ tissues. Current functionalities include (define-public r-trackviewer (package (name "r-trackviewer") - (version "1.38.1") + (version "1.38.2") (source (origin (method url-fetch) (uri (bioconductor-uri "trackViewer" version)) (sha256 (base32 - "008d1wg8882iq7jfmwijpchxrfva5ysl45ama62iy8s9dm0fpwsj")) + "1zgxp76ykgn4wk6nnpafjpswcky23jpghzzs68z0hhlzv4cc40s6")) (snippet '(delete-file "inst/htmlwidgets/lib/d3/d3.v4.min.js")))) (properties `((upstream-name . "trackViewer"))) @@ -12023,14 +12023,14 @@ of gene-level counts.") (define-public r-valr (package (name "r-valr") - (version "0.7.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "valr" version)) (sha256 (base32 - "038s5n8cbffpb9132rpw7q82cxfzlsc86fcywhv63c8szm5g9nrk")))) + "0jf47yfi8dr8mgqv1gbl2kd7wgyiwsnipiwfdhf9l346yg9aj96l")))) (build-system r-build-system) (propagated-inputs (list r-broom @@ -13006,18 +13006,19 @@ signals directly in the Bruker format.") (define-public r-codedepends (package (name "r-codedepends") - (version "0.6.5") + (version "0.6.6") (source (origin (method url-fetch) (uri (cran-uri "CodeDepends" version)) (sha256 (base32 - "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq")))) + "0msq5ksjqp2pjzl6f1vizw53gdf5lz520bpdr5dbjwz5mc1mp0bz")))) (properties `((upstream-name . "CodeDepends"))) (build-system r-build-system) (propagated-inputs (list r-codetools r-graph r-xml)) + (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/CodeDepends") (synopsis "Analysis of R code for reproducible research and code comprehension") (description @@ -14493,14 +14494,14 @@ single cell assay data.") (define-public r-monocle (package (name "r-monocle") - (version "2.30.0") + (version "2.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "monocle" version)) (sha256 (base32 - "0i1qnmiaf3gf8955nlqzd81xzg4siliq154k699jmsz0fyyykia1")))) + "0hb2s58xx5cmrn3wlppay7275mln8r5y5dsnvpcps3s6xcab00rm")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -14523,7 +14524,6 @@ single cell assay data.") r-pheatmap r-plyr r-proxy - r-qlcmatrix r-rann r-rcpp r-reshape2 @@ -15037,13 +15037,13 @@ standardization of the analyses and the development of best practices.") (define-public r-microbiomestat (package (name "r-microbiomestat") - (version "1.1") + (version "1.2") (source (origin (method url-fetch) (uri (cran-uri "MicrobiomeStat" version)) (sha256 (base32 - "1j5sar85a1gksc83pc4ypxwb0c7whxglx069zarphrgqfazcr1m4")))) + "1kpc68sl63k104xy7r6f3gxan0yx0rs7ksn8ldbq8xla00ddflgq")))) (properties `((upstream-name . "MicrobiomeStat"))) (build-system r-build-system) (propagated-inputs (list r-foreach @@ -15054,7 +15054,6 @@ standardization of the analyses and the development of best practices.") r-matrix r-matrixstats r-modeest - r-phyloseq r-statmod)) (home-page "https://cran.r-project.org/package=MicrobiomeStat") (synopsis "Statistical methods for microbiome compositional data") @@ -17583,14 +17582,14 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "2.10.1") + (version "2.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "044kh1rfgb608y2v4wzbzddirhw5crj3k6i28wr78qgnzqc89mdm")))) + "00gnnc4yypvjnvh1xq4bzqi34j9i9ld1rnjnb2gsxbhaq5nzq31z")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs @@ -18313,14 +18312,14 @@ interact with gated cytometry data.") (define-public r-flowcore (package (name "r-flowcore") - (version "2.14.1") + (version "2.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 - "1g6qxzvzn1gnmqba150lj9nb6wlrdpzkc61l77d3fkzaf0q1h1n7")))) + "1q47c6pyvcglxs1qga2814b7i84kmm5sncsnl0fhpa9zhx1sjka5")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs @@ -18500,14 +18499,14 @@ model with Box-Cox transformation.") (define-public r-rprotobuflib (package (name "r-rprotobuflib") - (version "2.14.0") + (version "2.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "RProtoBufLib" version)) (sha256 (base32 - "1i1a4ikfdyrrn0r53y1aipfm9dzzn6yzp5w651hvd6zav77cdh6q")))) + "015yaci2wimax2p772mndmy76qsj307rk4y71r5s8jcb0nwr0qg2")))) (properties `((upstream-name . "RProtoBufLib"))) (build-system r-build-system) (arguments @@ -18529,14 +18528,14 @@ for other R packages to compile and link against.") (define-public r-flowworkspace (package (name "r-flowworkspace") - (version "4.14.2") + (version "4.14.3") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 - "0rbhpvnx71djy893cb1b1qywm5aq8ad8rxjd0lqkylp13w7zv0g6")))) + "07hnzvzis6425j5kabdrp49wicd331k7kmkk2r7ydchxxlndz3ww")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (propagated-inputs @@ -20753,14 +20752,14 @@ rownames.") (define-public r-bioconcotk (package (name "r-bioconcotk") - (version "1.22.0") + (version "1.22.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocOncoTK" version)) (sha256 (base32 - "1xymgfiv9abyaq5s7m683ml8a1ls9mqvbh9qjiz3jqbbpvmsm502")))) + "0yx32yj9bw78nhbv1yvgs26sxdmnava1a89g9hs4ai26c1hy150s")))) (properties `((upstream-name . "BiocOncoTK"))) (build-system r-build-system) (propagated-inputs @@ -22404,14 +22403,14 @@ relevant, and the minimum expression of the most abundant condition.") (define-public r-catalyst (package (name "r-catalyst") - (version "1.26.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "CATALYST" version)) (sha256 (base32 - "0dfg9ib0imk8bmhycqrspnn8yvfdlchwvx39wgqxi5fb9zrppfz4")))) + "1zfb4b88j0ksvsxq8kgrjs0xqlr10yzvr772r8nhl797qzwdag08")))) (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs @@ -22869,14 +22868,14 @@ on the plot.") (define-public r-abn (package (name "r-abn") - (version "3.0.4") + (version "3.0.6") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 - "1qqsm6ldbf6rnzvspcnv87l4mkxccg4divzf6nj7j92jnhyadqia")))) + "0833070j4q553kc4g5wydln3q63g0igaam9h3rbylxcs0p1v2psj")))) (build-system r-build-system) (inputs (list gsl)) @@ -22893,7 +22892,7 @@ on the plot.") r-rjags r-stringi)) (native-inputs - (list r-r-rsp)) + (list r-knitr)) (home-page "https://r-bayesian-networks.org/") (synopsis "Modelling multivariate data with additive bayesian networks") (description @@ -23975,14 +23974,14 @@ using aCGH or sequencing.") (define-public r-bionero (package (name "r-bionero") - (version "1.10.1") + (version "1.10.3") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNERO" version)) (sha256 (base32 - "0dxn4pijr6gsqybl8x3ix1xydizg7gzfp72risk37zc5i4xk2lca")))) + "1vf3kq4lj4alvwzf0wl09lxb0ky6q0x94ajmrnihlj5saliqb73c")))) (properties `((upstream-name . "BioNERO"))) (build-system r-build-system) (propagated-inputs @@ -24470,13 +24469,13 @@ estimates, etc.") (define-public r-tcgabiolinks (package (name "r-tcgabiolinks") - (version "2.30.0") + (version "2.30.4") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAbiolinks" version)) (sha256 - (base32 "1k8xiv4bmil420176ckfda2r6y0s46dk1cm8dbywav86q28bmzzx")))) + (base32 "0br0bgcvxxfy1vclfc8i20b0bsb7rcchwfdx7lkw4f2aqxny8ja8")))) (properties `((upstream-name . "TCGAbiolinks"))) (build-system r-build-system) (propagated-inputs |