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-rw-r--r--gnu/packages/bioconductor.scm45
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)))))))