diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 46 |
1 files changed, 37 insertions, 9 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e2b4f6ea7f..c1da8ac106 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -694,6 +694,34 @@ annotations.") "This is a manifest package for Illumina's EPIC methylation arrays.") (license license:artistic2.0))) +;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19 +;; from Bioconductor. +(define-public r-deconstructsigs + (package + (name "r-deconstructsigs") + (version "1.8.0") + (source (origin + (method url-fetch) + (uri (cran-uri "deconstructSigs" version)) + (sha256 + (base32 + "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a")))) + (properties + `((upstream-name . "deconstructSigs"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bsgenome" ,r-bsgenome) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-reshape2" ,r-reshape2))) + (home-page "https://github.com/raerose01/deconstructSigs") + (synopsis "Identifies signatures present in a tumor sample") + (description "This package takes sample information in the form of the +fraction of mutations in each of 96 trinucleotide contexts and identifies +the weighted combination of published signatures that, when summed, most +closely reconstructs the mutational profile.") + (license license:gpl2+))) + (define-public r-do-db (package (name "r-do-db") @@ -2160,14 +2188,14 @@ possible, parallelization is achieved using the BiocParallel framework.") (define-public r-destiny (package (name "r-destiny") - (version "3.0.0") + (version "3.0.1") (source (origin (method url-fetch) (uri (bioconductor-uri "destiny" version)) (sha256 (base32 - "0vj9nk8g6i4vzm6cnzvbsqcvyk6fhmx0a0nxxrciarffyhqk81yz")))) + "1hzg53p1cz21bvnfyyz40bpvjhg89zi3rahlqf0c4w85iwc1i4vi")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -3165,14 +3193,14 @@ are standardized and usable by the accompanying mutossGUI package.") (define-public r-metap (package (name "r-metap") - (version "1.2") + (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "metap" version)) (sha256 (base32 - "0pfbcixjrzx81l9wqhlp55khg9k63zf8pvg2n39c19akr4ppzhvf")))) + "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) @@ -5164,14 +5192,14 @@ packages.") (define-public r-ropls (package (name "r-ropls") - (version "1.18.6") + (version "1.18.8") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "1sm2fmygrra9gdcs90lmk5y1ag6arga6159kggx4ij8bkhyc66vb")))) + "033i39r4037nd54jnp5zdn1vpzh61r671vmq0sf8dqrfblhm4w7a")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -7177,14 +7205,14 @@ access.") (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") - (version "1.12.1") + (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiAssayExperiment" version)) (sha256 (base32 - "0xpi5qpffg9pn8szkvicpc43a0r534wngyqwvsip8w66zi8c9kpc")))) + "0722f3jl1xq8k8w7vrv986jd16bgysqp3n07pgmdn0hh1zh2mcqc")))) (properties `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) @@ -7349,7 +7377,7 @@ analytics on packages.") (description "BiocSet displays different biological sets in a triple tibble format. These three tibbles are @code{element}, @code{set}, and @code{elementset}. -The user has the abilty to activate one of these three tibbles to perform +The user has the ability to activate one of these three tibbles to perform common functions from the @code{dplyr} package. Mapping functionality and accessing web references for elements/sets are also available in BiocSet.") (license license:artistic2.0))) |