diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 45 |
1 files changed, 34 insertions, 11 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1adf47b08f..74620a2cbe 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -38,7 +38,8 @@ #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages statistics) - #:use-module (gnu packages web)) + #:use-module (gnu packages web) + #:use-module (srfi srfi-1)) ;;; Annotations @@ -1211,14 +1212,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.18.1") + (version "3.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "1mwi5s600c3jxy8f1azfrndc3g06qvhbmrp9wqac9nwjbfx1kfji")))) + "0wzwdxvvr7wknz5jnan0wsp81c1gv4d2qx0mrb1yybqf4z068779")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -1520,14 +1521,14 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "0ipvm3c1cqd46n60lsrqzf6fx4b3lwia57jyfx9wcqqg205qj73b")))) + "0hq2n5yfr9h2ayn10dy9lz08gd2q0awrm5cy2kqdmz4d8ss4r94p")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) @@ -3528,14 +3529,14 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.8.1") + (version "1.8.5") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "0h5j3724hnd86w22vy3whqx6gkf0nf2dxd2clgzdvjzblbcd5s69")))) + "1i8f0vs0z4jbc2yvj1diay7jhcmb1a82zv96xllk771f25nvmmxp")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs @@ -3620,14 +3621,14 @@ annotations and ontologies.") (define-public r-abaenrichment (package (name "r-abaenrichment") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ABAEnrichment" version)) (sha256 (base32 - "0av1dysk7qa8c4a0pp7yq89k8c4y40d2gyvsb8f27slvv2i3aad2")))) + "1w322wsp6bd3gyfwzgdf088cvfmpq774knr57d0dj420ljf4xn48")))) (properties `((upstream-name . "ABAEnrichment"))) (build-system r-build-system) (propagated-inputs @@ -4840,14 +4841,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "1.34.4") + (version "1.34.6") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "1230p8nsakifmpsqfiaj8rpm7npa8ab903mfjmayfa71n6yzvcbs")))) + "0nnfh4hnrs5kd72m8c50cidbsxjz12szw2vynpmg8q0wpd99q550")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -5128,3 +5129,25 @@ data, to only emphasize the data that actually matters.") accessibility data. It also extends the monocle package for use in chromatin accessibility data.") (license license:expat))) + +;; This is the latest commit on the "monocle3" branch. +(define-public r-cicero-monocle3 + (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b") + (revision "1")) + (package (inherit r-cicero) + (name "r-cicero-monocle3") + (version (git-version "1.3.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/cole-trapnell-lab/cicero-release.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c")))) + (propagated-inputs + `(("r-monocle3" ,r-monocle3) + ,@(alist-delete "r-monocle" + (package-propagated-inputs r-cicero))))))) |