diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 115 |
1 files changed, 102 insertions, 13 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6210a4b3f1..a9f8ff21c5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org> ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com> +;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -1762,6 +1763,7 @@ expressed genes in DNA microarray experiments.") fitting of some classes of graphical Markov models.") (license license:gpl2+))) +;; This is a CRAN package, but it depends on a Bioconductor package. (define-public r-codedepends (package (name "r-codedepends") @@ -1793,14 +1795,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.22.2") + (version "3.22.3") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "199mlg0gwjy39afyk0ah6lzcm759bzxla4hgcajj0ay9jiibjqpa")))) + "0q3f55hh0a2hl96272js6gagmgps9cxs8s13pf6fii64rzaz5m7y")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -3452,14 +3454,14 @@ surface of a flowcell.") (define-public r-gkmsvm (package (name "r-gkmsvm") - (version "0.80.0") + (version "0.81.0") (source (origin (method url-fetch) (uri (cran-uri "gkmSVM" version)) (sha256 (base32 - "0ljcga246ad0ql8x3drvrdsyp0f20mgp3p6lnl79xb76qgfdnm0p")))) + "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj")))) (properties `((upstream-name . "gkmSVM"))) (build-system r-build-system) (propagated-inputs @@ -4360,14 +4362,14 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.12.3") + (version "1.12.4") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "12710c4024pndwwqiiqr6dhrd360z26fc8r3fxhs739gyd0ddk9r")))) + "1gs9862hhh4gr1akij6ykhcj29s9dzg1vnj87hqrm19dfgl43qbh")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs @@ -6334,14 +6336,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.12.1") + (version "6.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "13kq9l5xwhwp30y5gfqfh5f11n63vn8rk195mb2y2mww4cwi6lv4")))) + "1nkqlvm9j1f4vfj3f3kyxqgan38rpa9imimvl9pwivvsfl647vvc")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs @@ -6460,14 +6462,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-cicero (package (name "r-cicero") - (version "1.6.1") + (version "1.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "0nf9yqg5krj26n4n82iyx3rsr84d46b17i9zfk35sh12l4xssbii")))) + "042ba6yfa7fksij2v7cwnp2sca3vmz7izn6fsxx9xswnncrkgcqh")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) @@ -7157,14 +7159,14 @@ data.") (define-public r-activedriverwgs (package (name "r-activedriverwgs") - (version "1.0.1") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "ActiveDriverWGS" version)) (sha256 (base32 - "08l9dj8d3cd74z1dqn8n4yqykwvqjxsfa067wnxyh7xnfvvnm5v1")))) + "0l6h0f54zjvcx19ngq3kp01dypsjqf28vssjm8yzccmpyacfypag")))) (properties `((upstream-name . "ActiveDriverWGS"))) (build-system r-build-system) @@ -7175,8 +7177,9 @@ data.") ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) - ("r-plyr" ,r-plyr) ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/") (synopsis "Driver discovery tool for cancer whole genomes") (description @@ -8153,3 +8156,89 @@ user's input and automatically retrieving results from GREAT web server.") simulation to eliminate overestimation of @code{K} and can reject the null hypothesis @code{K=1}.") (license license:agpl3+))) + +(define-public r-icens + (package + (name "r-icens") + (version "1.60.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Icens" version)) + (sha256 + (base32 + "0fh7wgkrw20f61p06i87nccnbig9wv4m0jcg7cx1rw7g2ndnabgp")))) + (properties `((upstream-name . "Icens"))) + (build-system r-build-system) + (propagated-inputs + `(("r-survival" ,r-survival))) + (home-page "https://bioconductor.org/packages/Icens") + (synopsis "NPMLE for censored and truncated data") + (description + "This package provides many functions for computing the +@dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and +truncated data.") + (license license:artistic2.0))) + +;; This is a CRAN package but it depends on r-icens, which is published on +;; Bioconductor. +(define-public r-interval + (package + (name "r-interval") + (version "1.1-0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "interval" version)) + (sha256 + (base32 + "1lln9jkli28i4wivwzqrsxvv2n15560f7msjy5gssrm45vxrxms8")))) + (properties `((upstream-name . "interval"))) + (build-system r-build-system) + (propagated-inputs + `(("r-icens" ,r-icens) + ("r-mlecens" ,r-mlecens) + ("r-perm" ,r-perm) + ("r-survival" ,r-survival))) + (home-page "https://cran.r-project.org/web/packages/interval/") + (synopsis "Weighted Logrank tests and NPMLE for interval censored data") + (description + "This package provides functions to fit nonparametric survival curves, +plot them, and perform logrank or Wilcoxon type tests.") + (license license:gpl2+))) + +;; This is a CRAN package, but it depends on r-interval, which depends on a +;; Bioconductor package. +(define-public r-fhtest + (package + (name "r-fhtest") + (version "1.4") + (source + (origin + (method url-fetch) + (uri (cran-uri "FHtest" version)) + (sha256 + (base32 + "1wsn0j9ydpp9nfswiqg21p09kgkvaq8fh0y0h8syqgizah7i8vs2")))) + (properties `((upstream-name . "FHtest"))) + (build-system r-build-system) + (propagated-inputs + `(("r-interval" ,r-interval) + ("r-kmsurv" ,r-kmsurv) + ("r-mass" ,r-mass) + ("r-perm" ,r-perm) + ("r-survival" ,r-survival))) + (home-page "https://cran.r-project.org/web/packages/FHtest/") + (synopsis "Tests for survival data based on the Fleming-Harrington class") + (description + "This package provides functions to compare two or more survival curves +with: + +@itemize +@item The Fleming-Harrington test for right-censored data based on + permutations and on counting processes. +@item An extension of the Fleming-Harrington test for interval-censored data + based on a permutation distribution and on a score vector distribution. +@end itemize +") + (license license:gpl2+))) |