diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 101 |
1 files changed, 93 insertions, 8 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 86c303f2b1..2c8dc8f399 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8818,18 +8818,17 @@ replacement for strverscmp.") (define-public multiqc (package (name "multiqc") - (version "1.3") + (version "1.4") (source (origin (method url-fetch) (uri (pypi-uri "multiqc" version)) (sha256 (base32 - "0fx1sx53znbgzfhbbiyd8j6cg5llpcsl5q5c45jy2c81d12piqfd")))) + "0ihx4rzmsfphv4byn05qv6f1y95g2dxs6viwziipl4wjk96acgm8")))) (build-system python-build-system) (propagated-inputs - `(("python-enum34" ,python-enum34) - ("python-jinja2" ,python-jinja2) + `(("python-jinja2" ,python-jinja2) ("python-simplejson" ,python-simplejson) ("python-pyyaml" ,python-pyyaml) ("python-click" ,python-click) @@ -10627,6 +10626,67 @@ cell-specific biases, assignment of cell cycle phase, and detection of highly variable and significantly correlated genes.") (license license:gpl3))) +(define-public r-delayedmatrixstats + (package + (name "r-delayedmatrixstats") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DelayedMatrixStats" version)) + (sha256 + (base32 + "1nfdan0k2z4mynxyblsil0cjclsy63b0w9r1hczfk27i8hmxx13h")))) + (properties + `((upstream-name . "DelayedMatrixStats"))) + (build-system r-build-system) + (propagated-inputs + `(("r-delayedarray" ,r-delayedarray) + ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) + ("r-matrixstats" ,r-matrixstats) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://github.com/PeteHaitch/DelayedMatrixStats") + (synopsis "Functions that apply to rows and columns of DelayedMatrix objects") + (description + "This package provides a port of the @code{matrixStats} API for use with +@code{DelayedMatrix} objects from the @code{DelayedArray} package. It +contains high-performing functions operating on rows and columns of +@code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians}, +@code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions +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-dropbead + (let ((commit "cf0be5ae5302684bd03e78ab65b142900bbbb840") + (revision "1")) + (package + (name "r-dropbead") + (version (string-append "0-" revision "." (string-take commit 7))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rajewsky-lab/dropbead.git") + (commit commit))) + (sha256 + (base32 + "1b2lphsc236s1rdzlijxg8yl1jnqpwcvj4x938r89rqpj93jb780")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-gridextra" ,r-gridextra) + ("r-gplots" ,r-gplots) + ("r-plyr" ,r-plyr))) + (home-page "https://github.com/rajewsky-lab/dropbead") + (synopsis "Basic exploration and analysis of Drop-seq data") + (description "This package offers a quick and straight-forward way to +explore and perform basic analysis of single cell sequencing data coming from +droplet sequencing. It has been particularly tailored for Drop-seq.") + (license license:gpl3)))) + (define htslib-for-sambamba (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) (package @@ -10942,10 +11002,7 @@ programs for inferring phylogenies (evolutionary trees).") (arguments `(;; FIXME: Some tests fail because they produce warnings, others fail ;; because the PYTHONPATH does not include the modeller's directory. - #:tests? #f - ;; Do not place libraries in an architecture-specific directory. - #:configure-flags - (list "-DCMAKE_INSTALL_LIBDIR=lib"))) + #:tests? #f)) (inputs `(("boost" ,boost) ("gsl" ,gsl) @@ -11800,3 +11857,31 @@ use of lightweight alignments (accurate but fast-to-compute proxies for traditional read alignments) and massively-parallel stochastic collapsed variational inference.") (license license:gpl3+))) + +(define-public python-loompy + (package + (name "python-loompy") + (version "2.0.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "loompy" version)) + (sha256 + (base32 + "1drgv8j1hxqzzpnfg272x9djb6j8qr798w1pc2x8ikmfgyd9gh51")))) + (build-system python-build-system) + ;; There are no tests + (arguments '(#:tests? #f)) + (propagated-inputs + `(("python-h5py" ,python-h5py) + ("python-numpy" ,python-numpy) + ("python-scipy" ,python-scipy) + ("python-typing" ,python-typing))) + (home-page "https://github.com/linnarsson-lab/loompy") + (synopsis "Work with .loom files for single-cell RNA-seq data") + (description "The loom file format is an efficient format for very large +omics datasets, consisting of a main matrix, optional additional layers, a +variable number of row and column annotations. Loom also supports sparse +graphs. This library makes it easy to work with @file{.loom} files for +single-cell RNA-seq data.") + (license license:bsd-3))) |