diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 112 |
1 files changed, 109 insertions, 3 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7dbebcf3da..f75254ed9f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2110,6 +2110,29 @@ matplotlib Axes objects, making them easy to style and incorporate into multi-panel figures.") (license license:expat))) +(define-public python-parabam + (package + (name "python-parabam") + (version "3.0.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "parabam" version)) + (sha256 + (base32 "1cy9q3gzdawi1kilycpd7waymjmrwsg8czwycfp13g301ir9xyp3")) + (modules '((guix build utils))) + (snippet + '(substitute* "setup.py" + (("'argparse',") ""))))) + (build-system pyproject-build-system) + (propagated-inputs (list python-numpy python-pysam)) + (home-page "https://github.com/cancerit/parabam") + (synopsis "Parallel BAM File Analysis") + (description "Parabam is a tool for processing sequencing files in +parallel. It uses Python's native multiprocessing framework to apply a user +defined rule on an input file.") + (license license:gpl3))) + (define-public python-peaks2utr (package (name "python-peaks2utr") @@ -2424,6 +2447,30 @@ operations: @end itemize") (license license:asl2.0))) +(define-public python-telomerecat + (package + (name "python-telomerecat") + (version "4.0.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "telomerecat" version)) + (sha256 + (base32 "16mfdqmp0j6g3h26h59334w9lqb4qihqrlzwvgznj0fiqs1rkxn2")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-click python-numpy python-pandas + python-parabam python-pysam)) + (home-page "https://github.com/cancerit/telomerecat") + (synopsis "Telomere computational analysis tool") + (description "Telomerecat is a tool for estimating the average telomere +length (TL) for a paired end, whole genome sequencing (WGS) sample. + +Telomerecat is adaptable, accurate and fast. The algorithm accounts for +sequencing amplification artifacts, anneouploidy (common in cancer samples) +and noise generated by WGS. For a high coverage WGS BAM file of around 100GB +telomerecat can produce an estimate in ~1 hour.") + (license license:gpl3))) + (define-public python-bioframe (package (name "python-bioframe") @@ -11124,6 +11171,65 @@ single-cell data.") "This package is designed to streamline scATAC analyses in R.") (license license:gpl2+)))) +(define-public r-azimuth + (let ((commit "243ee5db80fcbffa3452c944254a325a3da2ef9e") + (revision "1")) + (package + (name "r-azimuth") + (version (git-version "0.5.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/satijalab/azimuth") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0vs4813kf2cv2j1z800ihwk62bw4dgmwgkd47rln58581chv39zm")))) + (properties `((upstream-name . "Azimuth"))) + (build-system r-build-system) + (propagated-inputs (list r-bsgenome-hsapiens-ucsc-hg38 + r-dt + r-ensdb-hsapiens-v86 + r-future + r-ggplot2 + r-glmgampoi + r-googlesheets4 + r-hdf5r + r-htmltools + r-httr + r-jaspar2020 + r-jsonlite + r-matrix + r-patchwork + r-plotly + r-presto + r-rcpp + r-rlang + r-scales + r-seurat + r-seuratdata + r-seuratdisk + r-seuratobject + r-shiny + r-shinybs + r-shinydashboard + r-shinyjs + r-signac + r-stringr + r-tfbstools + r-withr)) + (home-page "https://github.com/satijalab/azimuth") + (synopsis + "Shiny app showcasing a single-cell data query-reference mapping algorithm") + (description "Azimuth utilizes an annotated reference dataset. It +automates the processing, analysis, and interpretation. This applies +specifically to new single-cell RNA-seq or ATAC-seq experiments. Azimuth +leverages a reference-based mapping pipeline that inputs acounts matrix and +performs normalization, visualization, cell annotation, and differential +expression.") + (license license:gpl3)))) + (define-public r-icellnet ;; v1.0 tagged in 2020, last commit contains many fixes. ;; DESCRIPTION says Version: 0.0.0.9000. @@ -20309,11 +20415,11 @@ translates between different variant encodings.") (license license:asl2.0)))) (define-public r-signac - (let ((commit "af4142724b72574d957f7fe3d422ed5828ec3ad0") + (let ((commit "8ecdde291676102bb3b503f48926c993354b5471") (revision "1")) (package (name "r-signac") - (version (git-version "1.9.0" revision commit)) + (version (git-version "1.12.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference @@ -20322,7 +20428,7 @@ translates between different variant encodings.") (file-name (git-file-name name version)) (sha256 (base32 - "0ps0lp1dcy20r6lakil6ih81m04r0s6fnirvfjf01sfs0gsyddww")))) + "0idkcqb1i13m164nxbdwgs3vflw0cxzm2ir84aw0i811vx9lqz8c")))) (properties `((upstream-name . "Signac"))) (build-system r-build-system) (inputs (list zlib)) |