From ad8f46c69efd24915d380dba663c9f24746de1fc Mon Sep 17 00:00:00 2001 From: zimoun Date: Wed, 24 Jul 2019 20:21:56 +0200 Subject: gnu: Add r-all. * gnu/packages/bioconductor.scm (r-all): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e5a2d66b2d..649b64a4d7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -865,6 +865,34 @@ which were then sequenced to a depth of ~4 million reads per library, resulting in a complete gene expression profile for each cell.") (license license:artistic2.0))) +(define-public r-all + (package + (name "r-all") + (version "1.26.0") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/experiment/" instead of "bioc/". + (uri (string-append "https://www.bioconductor.org/packages/" + "release/data/experiment/src/contrib/" + "ALL_" version ".tar.gz")) + (sha256 + (base32 + "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9")))) + (properties `((upstream-name . "ALL"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase))) + (home-page "https://bioconductor.org/packages/ALL") + (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory") + (description + "The data consist of microarrays from 128 different individuals with +@dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates +are available. The data have been normalized (using rma) and it is the +jointly normalized data that are available here. The data are presented in +the form of an @code{exprSet} object.") + (license license:artistic2.0))) + ;;; Packages -- cgit v1.2.3 From a6fedf1f37dd031829caae0b743016cd5d52f06c Mon Sep 17 00:00:00 2001 From: zimoun Date: Wed, 24 Jul 2019 20:21:57 +0200 Subject: gnu: Add r-flowcore. * gnu/packages/bioconductor.scm (r-flowcore): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 649b64a4d7..93dec5bd1d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4797,3 +4797,33 @@ read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. It can be applied to all major sequencing techologies and to both short and long sequence reads.") (license license:gpl3))) + +(define-public r-flowcore + (package + (name "r-flowcore") + (version "1.50.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowCore" version)) + (sha256 + (base32 + "0pvcyzycsmgc8iw60q9xnhllfan6ihwpz3gvk8h1n9jmhpxzylan")))) + (properties `((upstream-name . "flowCore"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-corpcor" ,r-corpcor) + ("r-graph" ,r-graph) + ("r-mass" ,r-mass) + ("r-matrixstats" ,r-matrixstats) + ("r-rcpp" ,r-rcpp) + ("r-rrcov" ,r-rrcov))) + (home-page "https://bioconductor.org/packages/flowCore") + (synopsis "Basic structures for flow cytometry data") + (description + "This package provides S4 data structures and basic functions to deal +with flow cytometry data.") + (license license:artistic2.0))) -- cgit v1.2.3 From a0422d18f10e0c3b7c43cd873a193404b11efbc3 Mon Sep 17 00:00:00 2001 From: zimoun Date: Wed, 24 Jul 2019 20:21:58 +0200 Subject: gnu: Add r-flowutils. * gnu/packages/bioconductor.scm (r-flowutils): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 93dec5bd1d..f7ae4bd86c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4798,6 +4798,32 @@ gene fusion discovery. It can be applied to all major sequencing techologies and to both short and long sequence reads.") (license license:gpl3))) +(define-public r-flowutils + (package + (name "r-flowutils") + (version "1.48.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowUtils" version)) + (sha256 + (base32 + "1r7b0rszdzjq7jphh65p5m4x5ps0zbbagxl26gn2mapbjdyb47rm")))) + (properties `((upstream-name . "flowUtils"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-corpcor" ,r-corpcor) + ("r-flowcore" ,r-flowcore) + ("r-graph" ,r-graph) + ("r-runit" ,r-runit) + ("r-xml" ,r-xml))) + (home-page "https://github.com/jspidlen/flowUtils") + (synopsis "Utilities for flow cytometry") + (description + "This package provides utilities for flow cytometry data.") + (license license:artistic2.0))) + (define-public r-flowcore (package (name "r-flowcore") -- cgit v1.2.3 From ed6f49fc415a3af5b69a4054100e709354b031d0 Mon Sep 17 00:00:00 2001 From: zimoun Date: Wed, 24 Jul 2019 20:21:59 +0200 Subject: gnu: Add r-consensusclusterplus. * gnu/packages/bioconductor.scm (r-consensusclusterplus): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f7ae4bd86c..0b968bb137 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4824,6 +4824,31 @@ and to both short and long sequence reads.") "This package provides utilities for flow cytometry data.") (license license:artistic2.0))) +(define-public r-consensusclusterplus + (package + (name "r-consensusclusterplus") + (version "1.48.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ConsensusClusterPlus" version)) + (sha256 + (base32 + "1mlcm3wq5n8s0gxs35j0ph9576fhbrbrrsj2xy84fy20prcfs4w8")))) + (properties + `((upstream-name . "ConsensusClusterPlus"))) + (build-system r-build-system) + (propagated-inputs + `(("r-all" ,r-all) + ("r-biobase" ,r-biobase) + ("r-cluster" ,r-cluster))) + (home-page "https://bioconductor.org/packages/ConsensusClusterPlus") + (synopsis "Clustering algorithm") + (description + "This package provides an implementation of an algorithm for determining +cluster count and membership by stability evidence in unsupervised analysis.") + (license license:gpl2))) + (define-public r-flowcore (package (name "r-flowcore") -- cgit v1.2.3 From e0cb053edb34cd1cc74a5db1b6e59e6e16c2cfec Mon Sep 17 00:00:00 2001 From: zimoun Date: Wed, 24 Jul 2019 20:22:00 +0200 Subject: gnu: Add r-flowmeans. * gnu/packages/bioconductor.scm (r-flowmeans): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0b968bb137..ece5097940 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4878,3 +4878,29 @@ cluster count and membership by stability evidence in unsupervised analysis.") "This package provides S4 data structures and basic functions to deal with flow cytometry data.") (license license:artistic2.0))) + +(define-public r-flowmeans + (package + (name "r-flowmeans") + (version "1.44.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "flowMeans" version)) + (sha256 + (base32 + "0yp6y3mq5h4nf1d7ybqnriigwfmwanrqavpj3ry482sgiaip1hp2")))) + (properties `((upstream-name . "flowMeans"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-feature" ,r-feature) + ("r-flowcore" ,r-flowcore) + ("r-rrcov" ,r-rrcov))) + (home-page "https://bioconductor.org/packages/flowMeans") + (synopsis "Non-parametric flow cytometry data gating") + (description + "This package provides tools to identify cell populations in Flow +Cytometry data using non-parametric clustering and segmented-regression-based +change point detection.") + (license license:artistic2.0))) -- cgit v1.2.3 From 1502751b3220feda44e34c07c617086538ac1296 Mon Sep 17 00:00:00 2001 From: zimoun Date: Wed, 24 Jul 2019 20:22:02 +0200 Subject: gnu: Add r-flowsom. * gnu/packages/bioconductor.scm (r-flowsom): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ece5097940..ad48ccaebe 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4904,3 +4904,31 @@ with flow cytometry data.") Cytometry data using non-parametric clustering and segmented-regression-based change point detection.") (license license:artistic2.0))) + +(define-public r-flowsom + (package + (name "r-flowsom") + (version "1.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "FlowSOM" version)) + (sha256 + (base32 + "03wl3xk7g7vajc4kkrqa0gsbjfxlqr918qi849h5nir31963398l")))) + (properties `((upstream-name . "FlowSOM"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-consensusclusterplus" ,r-consensusclusterplus) + ("r-flowcore" ,r-flowcore) + ("r-flowutils" ,r-flowutils) + ("r-igraph" ,r-igraph) + ("r-tsne" ,r-tsne) + ("r-xml" ,r-xml))) + (home-page "https://bioconductor.org/packages/FlowSOM/") + (synopsis "Visualize and interpret cytometry data") + (description + "FlowSOM offers visualization options for cytometry data, by using +self-organizing map clustering and minimal spanning trees.") + (license license:gpl2+))) -- cgit v1.2.3 From 1adb9cbc5e9e4c458bbf3b3bb89fcd36278d34e2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Wed, 24 Jul 2019 20:22:03 +0200 Subject: gnu: Add r-mixomics. * gnu/packages/bioconductor.scm (r-mixomics): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ad48ccaebe..f63bfa4a1f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4932,3 +4932,45 @@ change point detection.") "FlowSOM offers visualization options for cytometry data, by using self-organizing map clustering and minimal spanning trees.") (license license:gpl2+))) + +(define-public r-mixomics + (package + (name "r-mixomics") + (version "6.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "mixOmics" version)) + (sha256 + (base32 + "1f08jx35amn3sfcmqb96mjxxsm6dnpzhff625z758x1992wj4zsk")))) + (properties `((upstream-name . "mixOmics"))) + (build-system r-build-system) + (propagated-inputs + `(("r-corpcor" ,r-corpcor) + ("r-dplyr" ,r-dplyr) + ("r-ellipse" ,r-ellipse) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-igraph" ,r-igraph) + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-matrixstats" ,r-matrixstats) + ("r-rarpack" ,r-rarpack) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-reshape2" ,r-reshape2) + ("r-tidyr" ,r-tidyr))) + (home-page "http://www.mixOmics.org") + (synopsis "Multivariate methods for exploration of biological datasets") + (description + "mixOmics offers a wide range of multivariate methods for the exploration +and integration of biological datasets with a particular focus on variable +selection. The package proposes several sparse multivariate models we have +developed to identify the key variables that are highly correlated, and/or +explain the biological outcome of interest. The data that can be analysed +with mixOmics may come from high throughput sequencing technologies, such as +omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but +also beyond the realm of omics (e.g. spectral imaging). The methods +implemented in mixOmics can also handle missing values without having to +delete entire rows with missing data.") + (license license:gpl2+))) -- cgit v1.2.3 From a0efa069a147f0e7b3bb305ae546609e9dd77045 Mon Sep 17 00:00:00 2001 From: zimoun Date: Wed, 24 Jul 2019 20:22:04 +0200 Subject: gnu: Add r-depecher. * gnu/packages/bioconductor.scm (r-depecher): New variable. Co-authored-by: Ricardo Wurmus Signed-off-by: Ricardo Wurmus --- gnu/packages/bioconductor.scm | 50 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f63bfa4a1f..2f2a60ad19 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4974,3 +4974,53 @@ also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data.") (license license:gpl2+))) + +(define-public r-depecher + (package + (name "r-depecher") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DepecheR" version)) + (sha256 + (base32 + "0qj2h2a50fncppvi2phh0mbivxkn1mv702mqpi9mvvkf3bzq8m0h")))) + (properties `((upstream-name . "DepecheR"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-syntax-error + (lambda _ + (substitute* "src/Makevars" + ((" & ") " && ")) + #t))))) + (propagated-inputs + `(("r-beanplot" ,r-beanplot) + ("r-biocparallel" ,r-biocparallel) + ("r-dosnow" ,r-dosnow) + ("r-dplyr" ,r-dplyr) + ("r-foreach" ,r-foreach) + ("r-ggplot2" ,r-ggplot2) + ("r-gplots" ,r-gplots) + ("r-mass" ,r-mass) + ("r-matrixstats" ,r-matrixstats) + ("r-mixomics" ,r-mixomics) + ("r-moments" ,r-moments) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-reshape2" ,r-reshape2) + ("r-viridis" ,r-viridis))) + (home-page "https://bioconductor.org/packages/DepecheR/") + (synopsis "Identify traits of clusters in high-dimensional entities") + (description + "The purpose of this package is to identify traits in a dataset that can +separate groups. This is done on two levels. First, clustering is performed, +using an implementation of sparse K-means. Secondly, the generated clusters +are used to predict outcomes of groups of individuals based on their +distribution of observations in the different clusters. As certain clusters +with separating information will be identified, and these clusters are defined +by a sparse number of variables, this method can reduce the complexity of +data, to only emphasize the data that actually matters.") + (license license:expat))) -- cgit v1.2.3 From b46a0ee7532639817fe846233a75c758a9e7b963 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 30 Jul 2019 15:22:40 +0200 Subject: gnu: Add r-cicero. * gnu/packages/bioconductor.scm (r-cicero): New variable. --- gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2f2a60ad19..98a2da21c9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5024,3 +5024,44 @@ with separating information will be identified, and these clusters are defined by a sparse number of variables, this method can reduce the complexity of data, to only emphasize the data that actually matters.") (license license:expat))) + +(define-public r-cicero + (package + (name "r-cicero") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "cicero" version)) + (sha256 + (base32 + "0f15l8zrh7l7nnvznb66116hvfk15djb9q240vbscm2w0y5fvkcr")))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) + ("r-fnn" ,r-fnn) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-glasso" ,r-glasso) + ("r-gviz" ,r-gviz) + ("r-igraph" ,r-igraph) + ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) + ("r-monocle" ,r-monocle) + ("r-plyr" ,r-plyr) + ("r-reshape2" ,r-reshape2) + ("r-s4vectors" ,r-s4vectors) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-vgam" ,r-vgam))) + (home-page "https://bioconductor.org/packages/cicero/") + (synopsis "Predict cis-co-accessibility from single-cell data") + (description + "Cicero computes putative cis-regulatory maps from single-cell chromatin +accessibility data. It also extends the monocle package for use in chromatin +accessibility data.") + (license license:expat))) -- cgit v1.2.3 From b2dce6b5a2eecb9e20e5ee03779c020b2644666b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 30 Jul 2019 15:52:48 +0200 Subject: gnu: Add r-monocle3. * gnu/packages/bioconductor.scm (r-monocle3): New variable. --- gnu/packages/bioconductor.scm | 63 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 63 insertions(+) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 98a2da21c9..1adf47b08f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -22,6 +22,7 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix build-system r) #:use-module (gnu packages) #:use-module (gnu packages base) @@ -2263,6 +2264,68 @@ tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.") (license license:artistic2.0))) +(define-public r-monocle3 + (package + (name "r-monocle3") + (version "0.1.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/cole-trapnell-lab/monocle3.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-delayedmatrixstats" ,r-delayedmatrixstats) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-grr" ,r-grr) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-igraph" ,r-igraph) + ("r-irlba" ,r-irlba) + ("r-limma" ,r-limma) + ("r-lmtest" ,r-lmtest) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-matrix-utils" ,r-matrix-utils) + ("r-pbapply" ,r-pbapply) + ("r-pbmcapply" ,r-pbmcapply) + ("r-pheatmap" ,r-pheatmap) + ("r-plotly" ,r-plotly) + ("r-pryr" ,r-pryr) + ("r-proxy" ,r-proxy) + ("r-pscl" ,r-pscl) + ("r-purrr" ,r-purrr) + ("r-rann" ,r-rann) + ("r-rcpp" ,r-rcpp) + ("r-rcppparallel" ,r-rcppparallel) + ("r-reshape2" ,r-reshape2) + ("r-reticulate" ,r-reticulate) + ("r-rhpcblasctl" ,r-rhpcblasctl) + ("r-rtsne" ,r-rtsne) + ("r-shiny" ,r-shiny) + ("r-slam" ,r-slam) + ("r-spdep" ,r-spdep) + ("r-speedglm" ,r-speedglm) + ("r-stringr" ,r-stringr) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) + ("r-uwot" ,r-uwot) + ("r-viridis" ,r-viridis))) + (home-page "https://github.com/cole-trapnell-lab/monocle3") + (synopsis "Analysis toolkit for single-cell RNA-Seq data") + (description + "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.") + (license license:expat))) + (define-public r-noiseq (package (name "r-noiseq") -- cgit v1.2.3 From 14bb1c4842eafdba9e646573101cb2335490ee01 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 31 Jul 2019 18:58:29 +0200 Subject: gnu: Add r-cicero-monocle3. * gnu/packages/bioconductor.scm (r-cicero-monocle3): New variable. --- gnu/packages/bioconductor.scm | 25 ++++++++++++++++++++++++- 1 file changed, 24 insertions(+), 1 deletion(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1adf47b08f..74af02a47d 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 @@ -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))))))) -- cgit v1.2.3