From 44f93ed6ed04bd1f47c86577568520584e207862 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Sat, 5 Sep 2020 22:32:33 +0200 Subject: gnu: seqmagick: Update to 0.8.0. * gnu/packages/bioinformatics.scm (seqmagick): Update to 0.8.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 893e3c2582..cab3df222c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6357,14 +6357,14 @@ bioinformatics file formats, sequence alignment, and more.") (define-public seqmagick (package (name "seqmagick") - (version "0.7.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (pypi-uri "seqmagick" version)) (sha256 (base32 - "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5")))) + "0pf98da7i59q47gwrbx0wjk6xlvbybiwphw80w7h4ydjj0579a2b")))) (build-system python-build-system) (inputs `(("python-biopython" ,python-biopython))) -- cgit 1.4.1 From 1f56ec08af704bdc7aa3e143bf5ce351c5306dea Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 9 Sep 2020 16:56:02 +0200 Subject: gnu: Add r-loomr. * gnu/packages/bioinformatics.scm (r-loomr): New variable. --- gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cab3df222c..f8792ef4d4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7808,6 +7808,32 @@ and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-loomr + (package + (name "r-loomr") + (version "0.2.0-beta") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/mojaveazure/loomR/archive/" + version ".tar.gz")) + (sha256 + (base32 + "1grchjgiky5siifkl9hmj6v0sf7q2by62rfdj2k8s2zhmrpgb0yw")))) + (build-system r-build-system) + (propagated-inputs + `(("r-hdf5r" ,r-hdf5r) + ("r-r6" ,r-r6) + ("r-iterators" ,r-iterators) + ("r-itertools" ,r-itertools) + ("r-matrix" ,r-matrix))) + (home-page "http://loompy.org") + (synopsis "R interface for loom files") + (description "This package provides an interface for the single-cell +RNAseq-oriented loom format. Loom files are an HDF5-based format for storing +and interacting with large single-cell RNAseq datasets.") + (license license:gpl3))) + (define-public r-xvector (package (name "r-xvector") -- cgit 1.4.1 From 0574446be82ef54b925441e4283bf754a86918a9 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 9 Sep 2020 17:02:55 +0200 Subject: gnu: Add r-bisquerna. * gnu/packages/bioinformatics.scm (r-bisquerna): New variable. --- gnu/packages/bioinformatics.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f8792ef4d4..9f2fd86de2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7923,6 +7923,31 @@ manipulating genomic intervals and variables defined along a genome.") on Bioconductor or which replace R functions.") (license license:artistic2.0))) +(define-public r-bisquerna + (package + (name "r-bisquerna") + (version "1.0.4") + (source (origin + (method url-fetch) + (uri (cran-uri "BisqueRNA" version)) + (sha256 + (base32 + "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2")))) + (properties `((upstream-name . "BisqueRNA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-limsolve" ,r-limsolve))) + (home-page "https://www.biorxiv.org/content/10.1101/669911v1") + (synopsis "Decomposition of Bulk Expression with Single-Cell Sequencing") + (description "This package provides tools to accurately estimate cell type +abundances from heterogeneous bulk expression. A reference-based method +utilizes single-cell information to generate a signature matrix and +transformation of bulk expression for accurate regression based estimates. +A marker-based method utilizes known cell-specific marker genes to measure +relative abundances across samples.") + (license license:gpl3))) + (define-public r-annotationdbi (package (name "r-annotationdbi") -- cgit 1.4.1 From 0f8db4dc88f2b0bfd50d10001b0a39c751a9c6c0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Sep 2020 18:14:48 +0200 Subject: Revert "gnu: Add r-loomr." This reverts commit 1f56ec08af704bdc7aa3e143bf5ce351c5306dea. This package is not free software. --- gnu/packages/bioinformatics.scm | 26 -------------------------- 1 file changed, 26 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9f2fd86de2..96cc71babc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7808,32 +7808,6 @@ and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) -(define-public r-loomr - (package - (name "r-loomr") - (version "0.2.0-beta") - (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/mojaveazure/loomR/archive/" - version ".tar.gz")) - (sha256 - (base32 - "1grchjgiky5siifkl9hmj6v0sf7q2by62rfdj2k8s2zhmrpgb0yw")))) - (build-system r-build-system) - (propagated-inputs - `(("r-hdf5r" ,r-hdf5r) - ("r-r6" ,r-r6) - ("r-iterators" ,r-iterators) - ("r-itertools" ,r-itertools) - ("r-matrix" ,r-matrix))) - (home-page "http://loompy.org") - (synopsis "R interface for loom files") - (description "This package provides an interface for the single-cell -RNAseq-oriented loom format. Loom files are an HDF5-based format for storing -and interacting with large single-cell RNAseq datasets.") - (license license:gpl3))) - (define-public r-xvector (package (name "r-xvector") -- cgit 1.4.1 From 66be746dc0c0f4ba3d748ed8d0983b2f9afdace8 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 10 Sep 2020 16:38:43 +0200 Subject: gnu: Move r-bisquerna. * gnu/packages/bioinformatics.scm (r-bisquerna): Move to ... * gnu/packages/cran.scm: ... here. --- gnu/packages/bioinformatics.scm | 25 ------------------------- gnu/packages/cran.scm | 25 +++++++++++++++++++++++++ 2 files changed, 25 insertions(+), 25 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 96cc71babc..cab3df222c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7897,31 +7897,6 @@ manipulating genomic intervals and variables defined along a genome.") on Bioconductor or which replace R functions.") (license license:artistic2.0))) -(define-public r-bisquerna - (package - (name "r-bisquerna") - (version "1.0.4") - (source (origin - (method url-fetch) - (uri (cran-uri "BisqueRNA" version)) - (sha256 - (base32 - "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2")))) - (properties `((upstream-name . "BisqueRNA"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-limsolve" ,r-limsolve))) - (home-page "https://www.biorxiv.org/content/10.1101/669911v1") - (synopsis "Decomposition of Bulk Expression with Single-Cell Sequencing") - (description "This package provides tools to accurately estimate cell type -abundances from heterogeneous bulk expression. A reference-based method -utilizes single-cell information to generate a signature matrix and -transformation of bulk expression for accurate regression based estimates. -A marker-based method utilizes known cell-specific marker genes to measure -relative abundances across samples.") - (license license:gpl3))) - (define-public r-annotationdbi (package (name "r-annotationdbi") diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8f7e379e42..27fae416f8 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -2183,6 +2183,31 @@ where the bound function accepts additional arguments.") bindings that call a C++ function.") (license license:expat))) +(define-public r-bisquerna + (package + (name "r-bisquerna") + (version "1.0.4") + (source (origin + (method url-fetch) + (uri (cran-uri "BisqueRNA" version)) + (sha256 + (base32 + "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2")))) + (properties `((upstream-name . "BisqueRNA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-limsolve" ,r-limsolve))) + (home-page "https://www.biorxiv.org/content/10.1101/669911v1") + (synopsis "Decomposition of bulk expression with single-cell sequencing") + (description "This package provides tools to accurately estimate cell type +abundances from heterogeneous bulk expression. A reference-based method +utilizes single-cell information to generate a signature matrix and +transformation of bulk expression for accurate regression based estimates. +A marker-based method utilizes known cell-specific marker genes to measure +relative abundances across samples.") + (license license:gpl3))) + (define-public r-auc (package (name "r-auc") -- cgit 1.4.1 From 496a52dc410e287aa2bd03e962fdc110cfb2a1cc Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 11 Sep 2020 20:08:42 +0200 Subject: gnu: r-qtl: Move to (gnu packages cran). * gnu/packages/bioinformatics.scm (r-qtl): Move from here... * gnu/packages/cran.scm (r-qtl): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioinformatics.scm | 25 ------------------------- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 2 files changed, 26 insertions(+), 25 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cab3df222c..ae728f09dc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8510,31 +8510,6 @@ Stephens (1990).") throughput genetic sequencing data sets using regression methods.") (license license:artistic2.0))) -(define-public r-qtl - (package - (name "r-qtl") - (version "1.46-2") - (source - (origin - (method url-fetch) - (uri (string-append "mirror://cran/src/contrib/qtl_" - version ".tar.gz")) - (sha256 - (base32 - "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a")))) - (build-system r-build-system) - (home-page "https://rqtl.org/") - (synopsis "R package for analyzing QTL experiments in genetics") - (description "R/qtl is an extension library for the R statistics -system. It is used to analyze experimental crosses for identifying -genes contributing to variation in quantitative traits (so-called -quantitative trait loci, QTLs). - -Using a hidden Markov model, R/qtl estimates genetic maps, to -identify genotyping errors, and to perform single-QTL and two-QTL, -two-dimensional genome scans.") - (license license:gpl3))) - (define-public r-qtl2 (package (name "r-qtl2") diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0d10793e9f..980ad17594 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus ;;; Copyright © 2015 Andreas Enge +;;; Copyright © 2015, 2016 Pjotr Prins ;;; Copyright © 2016, 2017 Ben Woodcroft ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice @@ -24330,3 +24331,28 @@ are tests where the test statistic is the sum of the product of a covariate (usually group indicator) and the scores.") ;; Any version of the GPL (license license:gpl2+))) + +(define-public r-qtl + (package + (name "r-qtl") + (version "1.46-2") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://cran/src/contrib/qtl_" + version ".tar.gz")) + (sha256 + (base32 + "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a")))) + (build-system r-build-system) + (home-page "https://rqtl.org/") + (synopsis "R package for analyzing QTL experiments in genetics") + (description "R/qtl is an extension library for the R statistics +system. It is used to analyze experimental crosses for identifying +genes contributing to variation in quantitative traits (so-called +quantitative trait loci, QTLs). + +Using a hidden Markov model, R/qtl estimates genetic maps, to +identify genotyping errors, and to perform single-QTL and two-QTL, +two-dimensional genome scans.") + (license license:gpl3))) -- cgit 1.4.1 From 66a8e620705d98b6240670f7f5f9441462e8f621 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 11 Sep 2020 20:08:43 +0200 Subject: gnu: r-qtl2: Move to (gnu packages cran). * gnu/packages/bioinformatics.scm (r-qtl2): Move from here... * gnu/packages/cran.scm (r-qtl2): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioinformatics.scm | 26 -------------------------- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 2 files changed, 27 insertions(+), 26 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ae728f09dc..4de52f3aaa 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8510,32 +8510,6 @@ Stephens (1990).") throughput genetic sequencing data sets using regression methods.") (license license:artistic2.0))) -(define-public r-qtl2 - (package - (name "r-qtl2") - (version "0.22-11") - (source (origin - (method url-fetch) - (uri (cran-uri "qtl2" version)) - (sha256 - (base32 "0dfdzjylqzc92dcszawc8cyinxccjm3p36v9vcq9ma818pqcanmr")))) - (build-system r-build-system) - (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-jsonlite" ,r-jsonlite) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rsqlite" ,r-rsqlite) - ("r-yaml" ,r-yaml))) - (home-page "https://kbroman.org/qtl2/") - (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses") - (description - "This package provides a set of tools to perform @dfn{Quantitative Trait -Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the -@code{R/qtl} package to better handle high-dimensional data and complex cross -designs. Broman et al. (2018) .") - (license license:gpl3))) - (define-public r-zlibbioc (package (name "r-zlibbioc") diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 980ad17594..57b68c26ed 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -19,6 +19,7 @@ ;;; Copyright © 2019 Nicolò Balzarotti ;;; Copyright © 2019 Wiktor Żelazny ;;; Copyright © 2019 Arne Babenhauserheide +;;; Copyright © 2019, 2020 Efraim Flashner ;;; Copyright © 2020 Todor Kondić ;;; Copyright © 2020 Danjela Lura ;;; Copyright © 2020 Naga Malleswari @@ -24356,3 +24357,29 @@ Using a hidden Markov model, R/qtl estimates genetic maps, to identify genotyping errors, and to perform single-QTL and two-QTL, two-dimensional genome scans.") (license license:gpl3))) + +(define-public r-qtl2 + (package + (name "r-qtl2") + (version "0.22-11") + (source (origin + (method url-fetch) + (uri (cran-uri "qtl2" version)) + (sha256 + (base32 "0dfdzjylqzc92dcszawc8cyinxccjm3p36v9vcq9ma818pqcanmr")))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-jsonlite" ,r-jsonlite) + ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) + ("r-rsqlite" ,r-rsqlite) + ("r-yaml" ,r-yaml))) + (home-page "https://kbroman.org/qtl2/") + (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses") + (description + "This package provides a set of tools to perform @dfn{Quantitative Trait +Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the +@code{R/qtl} package to better handle high-dimensional data and complex cross +designs. Broman et al. (2018) .") + (license license:gpl3))) -- cgit 1.4.1 From 30aaee33066b9479cfc353f97f5f83f2e64517ef Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 11 Sep 2020 20:08:44 +0200 Subject: gnu: r-seqminer: Move to (gnu packages cran). * gnu/packages/bioinformatics.scm (r-seqminer): Move from here... * gnu/packages/cran.scm (r-seqminer): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioinformatics.scm | 22 ---------------------- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 2 files changed, 22 insertions(+), 22 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4de52f3aaa..40c6363859 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9393,28 +9393,6 @@ imaging data that can be used in subsequent analyses to adjust for unknown, unmodeled, or latent sources of noise.") (license license:artistic2.0))) -(define-public r-seqminer - (package - (name "r-seqminer") - (version "8.0") - (source - (origin - (method url-fetch) - (uri (cran-uri "seqminer" version)) - (sha256 - (base32 - "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i")))) - (build-system r-build-system) - (inputs - `(("zlib" ,zlib))) - (home-page "http://seqminer.genomic.codes") - (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)") - (description - "This package provides tools to integrate nucleotide sequencing -data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.") - ;; Any version of the GPL is acceptable - (license (list license:gpl2+ license:gpl3+)))) - (define-public r-raremetals2 (package (name "r-raremetals2") diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 57b68c26ed..fec9947d0d 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24383,3 +24383,25 @@ Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the @code{R/qtl} package to better handle high-dimensional data and complex cross designs. Broman et al. (2018) .") (license license:gpl3))) + +(define-public r-seqminer + (package + (name "r-seqminer") + (version "8.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "seqminer" version)) + (sha256 + (base32 + "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i")))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (home-page "http://seqminer.genomic.codes") + (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)") + (description + "This package provides tools to integrate nucleotide sequencing +data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.") + ;; Any version of the GPL is acceptable + (license (list license:gpl2+ license:gpl3+)))) -- cgit 1.4.1 From b31c364467470a7d4f7eb46fb2c5ca13c9ec2121 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 11 Sep 2020 20:08:45 +0200 Subject: gnu: r-maldiquant: Move to (gnu packages cran). * gnu/packages/bioinformatics.scm (r-maldiquant): Move from here... * gnu/packages/cran.scm (r-maldiquant): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioinformatics.scm | 26 -------------------------- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 2 files changed, 26 insertions(+), 26 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 40c6363859..fecb3c072d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9425,32 +9425,6 @@ for analyzing gene-level association tests in meta-analyses for binary trait.") (license license:gpl3))) -(define-public r-maldiquant - (package - (name "r-maldiquant") - (version "1.19.3") - (source - (origin - (method url-fetch) - (uri (cran-uri "MALDIquant" version)) - (sha256 - (base32 - "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57")))) - (properties `((upstream-name . "MALDIquant"))) - (build-system r-build-system) - (home-page "https://cran.r-project.org/web/packages/MALDIquant") - (synopsis "Quantitative analysis of mass spectrometry data") - (description - "This package provides a complete analysis pipeline for matrix-assisted -laser desorption/ionization-time-of-flight (MALDI-TOF) and other -two-dimensional mass spectrometry data. In addition to commonly used plotting -and processing methods it includes distinctive features, namely baseline -subtraction methods such as morphological filters (TopHat) or the -statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak -alignment using warping functions, handling of replicated measurements as well -as allowing spectra with different resolutions.") - (license license:gpl3+))) - (define-public r-protgenerics (package (name "r-protgenerics") diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index fec9947d0d..3657ae1515 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24405,3 +24405,29 @@ designs. Broman et al. (2018) .") data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.") ;; Any version of the GPL is acceptable (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-maldiquant + (package + (name "r-maldiquant") + (version "1.19.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "MALDIquant" version)) + (sha256 + (base32 + "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57")))) + (properties `((upstream-name . "MALDIquant"))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/MALDIquant") + (synopsis "Quantitative analysis of mass spectrometry data") + (description + "This package provides a complete analysis pipeline for matrix-assisted +laser desorption/ionization-time-of-flight (MALDI-TOF) and other +two-dimensional mass spectrometry data. In addition to commonly used plotting +and processing methods it includes distinctive features, namely baseline +subtraction methods such as morphological filters (TopHat) or the +statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak +alignment using warping functions, handling of replicated measurements as well +as allowing spectra with different resolutions.") + (license license:gpl3+))) -- cgit 1.4.1 From f9c0b2e05a22cc7a6667437c20bc2984e73835ae Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 11 Sep 2020 20:08:46 +0200 Subject: gnu: r-seurat: Move to (gnu packages cran). * gnu/packages/bioinformatics.scm (r-seurat): Move from here... * gnu/packages/cran.scm (r-seurat): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioinformatics.scm | 65 ----------------------------------------- gnu/packages/cran.scm | 65 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 65 insertions(+), 65 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fecb3c072d..a6505099fc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9735,71 +9735,6 @@ contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.") (license license:artistic2.0))) -(define-public r-seurat - (package - (name "r-seurat") - (version "3.2.0") - (source (origin - (method url-fetch) - (uri (cran-uri "Seurat" version)) - (sha256 - (base32 - "1vj3dlsqakgnn4x1jz9fkl2cy0jzc5s65h1c20fnamr7lk45pnf2")))) - (properties `((upstream-name . "Seurat"))) - (build-system r-build-system) - (propagated-inputs - `(("r-ape" ,r-ape) - ("r-cluster" ,r-cluster) - ("r-cowplot" ,r-cowplot) - ("r-fitdistrplus" ,r-fitdistrplus) - ("r-future" ,r-future) - ("r-future-apply" ,r-future-apply) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-ggridges" ,r-ggridges) - ("r-httr" ,r-httr) - ("r-ica" ,r-ica) - ("r-igraph" ,r-igraph) - ("r-irlba" ,r-irlba) - ("r-jsonlite" ,r-jsonlite) - ("r-kernsmooth" ,r-kernsmooth) - ("r-leiden" ,r-leiden) - ("r-lmtest" ,r-lmtest) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-miniui" ,r-miniui) - ("r-patchwork" ,r-patchwork) - ("r-pbapply" ,r-pbapply) - ("r-plotly" ,r-plotly) - ("r-png" ,r-png) - ("r-rann" ,r-rann) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rcppannoy" ,r-rcppannoy) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rcppprogress" ,r-rcppprogress) - ("r-reticulate" ,r-reticulate) - ("r-rlang" ,r-rlang) - ("r-rocr" ,r-rocr) - ("r-rsvd" ,r-rsvd) - ("r-rtsne" ,r-rtsne) - ("r-scales" ,r-scales) - ("r-sctransform" ,r-sctransform) - ("r-shiny" ,r-shiny) - ("r-spatstat" ,r-spatstat) - ("r-tibble" ,r-tibble) - ("r-uwot" ,r-uwot))) - (home-page "http://www.satijalab.org/seurat") - (synopsis "Seurat is an R toolkit for single cell genomics") - (description - "This package is an R package designed for QC, analysis, and -exploration of single cell RNA-seq data. It easily enables widely-used -analytical techniques, including the identification of highly variable genes, -dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering -algorithms; density clustering, hierarchical clustering, k-means, and the -discovery of differentially expressed genes and markers.") - (license license:gpl3))) - (define-public r-aroma-light (package (name "r-aroma-light") diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3657ae1515..10d480a80c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24431,3 +24431,68 @@ statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.") (license license:gpl3+))) + +(define-public r-seurat + (package + (name "r-seurat") + (version "3.2.0") + (source (origin + (method url-fetch) + (uri (cran-uri "Seurat" version)) + (sha256 + (base32 + "1vj3dlsqakgnn4x1jz9fkl2cy0jzc5s65h1c20fnamr7lk45pnf2")))) + (properties `((upstream-name . "Seurat"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-cluster" ,r-cluster) + ("r-cowplot" ,r-cowplot) + ("r-fitdistrplus" ,r-fitdistrplus) + ("r-future" ,r-future) + ("r-future-apply" ,r-future-apply) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-ggridges" ,r-ggridges) + ("r-httr" ,r-httr) + ("r-ica" ,r-ica) + ("r-igraph" ,r-igraph) + ("r-irlba" ,r-irlba) + ("r-jsonlite" ,r-jsonlite) + ("r-kernsmooth" ,r-kernsmooth) + ("r-leiden" ,r-leiden) + ("r-lmtest" ,r-lmtest) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-miniui" ,r-miniui) + ("r-patchwork" ,r-patchwork) + ("r-pbapply" ,r-pbapply) + ("r-plotly" ,r-plotly) + ("r-png" ,r-png) + ("r-rann" ,r-rann) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcpp" ,r-rcpp) + ("r-rcppannoy" ,r-rcppannoy) + ("r-rcppeigen" ,r-rcppeigen) + ("r-rcppprogress" ,r-rcppprogress) + ("r-reticulate" ,r-reticulate) + ("r-rlang" ,r-rlang) + ("r-rocr" ,r-rocr) + ("r-rsvd" ,r-rsvd) + ("r-rtsne" ,r-rtsne) + ("r-scales" ,r-scales) + ("r-sctransform" ,r-sctransform) + ("r-shiny" ,r-shiny) + ("r-spatstat" ,r-spatstat) + ("r-tibble" ,r-tibble) + ("r-uwot" ,r-uwot))) + (home-page "http://www.satijalab.org/seurat") + (synopsis "Seurat is an R toolkit for single cell genomics") + (description + "This package is an R package designed for QC, analysis, and +exploration of single cell RNA-seq data. It easily enables widely-used +analytical techniques, including the identification of highly variable genes, +dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering +algorithms; density clustering, hierarchical clustering, k-means, and the +discovery of differentially expressed genes and markers.") + (license license:gpl3))) -- cgit 1.4.1 From 415aa8a583a018ed2dd7e97a2045e7bd03a67674 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 11 Sep 2020 20:08:49 +0200 Subject: gnu: r-phangorn: Move to (gnu packages cran). * gnu/packages/bioinformatics.scm (r-phangorn): Move from here... * gnu/packages/cran.scm (r-phangorn): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioinformatics.scm | 28 ---------------------------- gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++ 2 files changed, 28 insertions(+), 28 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a6505099fc..bec6c1dc4a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10936,34 +10936,6 @@ are optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized.") (license license:expat))) -(define-public r-phangorn - (package - (name "r-phangorn") - (version "2.5.5") - (source - (origin - (method url-fetch) - (uri (cran-uri "phangorn" version)) - (sha256 - (base32 - "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5")))) - (build-system r-build-system) - (propagated-inputs - `(("r-ape" ,r-ape) - ("r-fastmatch" ,r-fastmatch) - ("r-igraph" ,r-igraph) - ("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-quadprog" ,r-quadprog) - ("r-rcpp" ,r-rcpp))) - (home-page "https://github.com/KlausVigo/phangorn") - (synopsis "Phylogenetic analysis in R") - (description - "Phangorn is a package for phylogenetic analysis in R. It supports -estimation of phylogenetic trees and networks using Maximum Likelihood, -Maximum Parsimony, distance methods and Hadamard conjugation.") - (license license:gpl2+))) - (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 10d480a80c..a3808e9882 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24496,3 +24496,31 @@ dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering algorithms; density clustering, hierarchical clustering, k-means, and the discovery of differentially expressed genes and markers.") (license license:gpl3))) + +(define-public r-phangorn + (package + (name "r-phangorn") + (version "2.5.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "phangorn" version)) + (sha256 + (base32 + "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-fastmatch" ,r-fastmatch) + ("r-igraph" ,r-igraph) + ("r-magrittr" ,r-magrittr) + ("r-matrix" ,r-matrix) + ("r-quadprog" ,r-quadprog) + ("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/KlausVigo/phangorn") + (synopsis "Phylogenetic analysis in R") + (description + "Phangorn is a package for phylogenetic analysis in R. It supports +estimation of phylogenetic trees and networks using Maximum Likelihood, +Maximum Parsimony, distance methods and Hadamard conjugation.") + (license license:gpl2+))) -- cgit 1.4.1 From 77c73940867e4883e1433f0770d52fccf7e1ee12 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 11 Sep 2020 20:08:47 +0200 Subject: gnu: r-diversitree: Move to (gnu packages cran). * gnu/packages/bioinformatics.scm (r-diversitree): Move from here... * gnu/packages/cran.scm (r-diversitree): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioinformatics.scm | 31 ------------------------------- gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++ 2 files changed, 31 insertions(+), 31 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bec6c1dc4a..6381523009 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13084,37 +13084,6 @@ analyses in addition to large-scale sequence-level searches.") (supported-systems '("x86_64-linux")) (license license:bsd-3)))) -(define-public r-diversitree - (package - (name "r-diversitree") - (version "0.9-13") - (source - (origin - (method url-fetch) - (uri (cran-uri "diversitree" version)) - (sha256 - (base32 - "00vi4klywi35hd170ksjv3xja3hqqbkcidcnrrlpgv4179k0azix")))) - (build-system r-build-system) - (native-inputs - `(("gfortran" ,gfortran))) - (inputs `(("fftw" ,fftw) ("gsl" ,gsl))) - (propagated-inputs - `(("r-ape" ,r-ape) - ("r-desolve" ,r-desolve) - ("r-rcpp" ,r-rcpp) - ("r-subplex" ,r-subplex))) - (home-page "https://www.zoology.ubc.ca/prog/diversitree") - (synopsis "Comparative 'phylogenetic' analyses of diversification") - (description "This package contains a number of comparative \"phylogenetic\" -methods, mostly focusing on analysing diversification and character evolution. -Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction) -and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and -Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods -include Markov models of discrete and continuous trait evolution and constant -rate speciation and extinction.") - (license license:gpl2+))) - (define-public sjcount ;; There is no tag for version 3.2, nor is there a release archive. (let ((commit "292d3917cadb3f6834c81e509c30e61cd7ead6e5") diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a3808e9882..f483178656 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24524,3 +24524,34 @@ discovery of differentially expressed genes and markers.") estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation.") (license license:gpl2+))) + +(define-public r-diversitree + (package + (name "r-diversitree") + (version "0.9-13") + (source + (origin + (method url-fetch) + (uri (cran-uri "diversitree" version)) + (sha256 + (base32 + "00vi4klywi35hd170ksjv3xja3hqqbkcidcnrrlpgv4179k0azix")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (inputs `(("fftw" ,fftw) ("gsl" ,gsl))) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-desolve" ,r-desolve) + ("r-rcpp" ,r-rcpp) + ("r-subplex" ,r-subplex))) + (home-page "https://www.zoology.ubc.ca/prog/diversitree") + (synopsis "Comparative 'phylogenetic' analyses of diversification") + (description "This package contains a number of comparative \"phylogenetic\" +methods, mostly focusing on analysing diversification and character evolution. +Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction) +and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and +Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods +include Markov models of discrete and continuous trait evolution and constant +rate speciation and extinction.") + (license license:gpl2+))) -- cgit 1.4.1 From d4e2ec1b8ac1f80011807a90906e036971a45da5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 11 Sep 2020 20:08:48 +0200 Subject: gnu: r-absfiltergsea: Move to (gnu packages cran). * gnu/packages/bioinformatics.scm (r-absfiltergsea): Move from here... * gnu/packages/cran.scm (r-absfiltergsea): ...to here. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioinformatics.scm | 27 --------------------------- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 2 files changed, 27 insertions(+), 27 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6381523009..ffa2618458 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14083,33 +14083,6 @@ downstream analysis. Poretools operates directly on the native FAST5, a variant of the Hierarchical Data Format (HDF5) standard.") (license license:expat)))) -(define-public r-absfiltergsea - (package - (name "r-absfiltergsea") - (version "1.5.1") - (source - (origin - (method url-fetch) - (uri (cran-uri "AbsFilterGSEA" version)) - (sha256 - (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w")))) - (properties `((upstream-name . "AbsFilterGSEA"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-deseq" ,r-deseq) - ("r-limma" ,r-limma) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) - (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/") - (synopsis "Improved false positive control of gene-permuting with absolute filtering") - (description - "This package provides a function that performs gene-permuting of a gene-set -enrichment analysis (GSEA) calculation with or without the absolute filtering. - Without filtering, users can perform (original) two-tailed or one-tailed -absolute GSEA.") - (license license:gpl2))) - (define-public jamm (package (name "jamm") diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index f483178656..16983c85b4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24555,3 +24555,30 @@ Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods include Markov models of discrete and continuous trait evolution and constant rate speciation and extinction.") (license license:gpl2+))) + +(define-public r-absfiltergsea + (package + (name "r-absfiltergsea") + (version "1.5.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "AbsFilterGSEA" version)) + (sha256 + (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w")))) + (properties `((upstream-name . "AbsFilterGSEA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-deseq" ,r-deseq) + ("r-limma" ,r-limma) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo))) + (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/") + (synopsis "Improved false positive control of gene-permuting with absolute filtering") + (description + "This package provides a function that performs gene-permuting of a gene-set +enrichment analysis (GSEA) calculation with or without the absolute filtering. + Without filtering, users can perform (original) two-tailed or one-tailed +absolute GSEA.") + (license license:gpl2))) -- cgit 1.4.1