diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 484 |
1 files changed, 480 insertions, 4 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d684e4249b..f157523a76 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -719,6 +719,40 @@ suite native in R.") for all types of microbial diversity analyses.") (license license:expat)))) +(define-public r-codeandroll2 + (let ((commit "d58e258851a5c0b430e8620d34dbeefb597c548f") + (revision "1")) + (package + (name "r-codeandroll2") + (version (git-version "2.3.6" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vertesy/CodeAndRoll2") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0sy88mfgw6qqhpnlc5020qzr1jllkcrxfhl2lw42bkl5nb56is71")))) + (properties `((upstream-name . "CodeAndRoll2"))) + (build-system r-build-system) + (propagated-inputs (list r-colorramps + r-dplyr + r-gplots + r-gtools + r-plyr + r-rcolorbrewer + r-sessioninfo + r-sm + r-stringendo + r-stringr)) + (home-page "https://github.com/vertesy/CodeAndRoll2") + (synopsis "CodeAndRoll2 for vector, matrix and list manipulations") + (description + "CodeAndRoll2 is a set of more than 130 productivity functions. +These functions are used by MarkdownReports, ggExpress, and SeuratUtils.") + (license license:gpl3)))) + (define-public r-conospanel (let ((commit "39e76b201a783b4e92fd615010a735a61746fbb9") (revision "1")) @@ -743,6 +777,47 @@ each with 3000 cells. There are two samples which are bone marrow (BM), and two samples which are cord blood (CB).") (license license:gpl3)))) +(define-public r-conqur + (let ((commit "c7a88794efd4ecfe4d96988dceeec3b410222e48") + (revision "1")) + (package + (name "r-conqur") + (version (git-version "2.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/wdl2459/ConQuR") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "19a7p2l67mgjy99i5ksjxlhzaqmrnyi1vzvwnhgnx2jrr6crj7rq")))) + (properties `((upstream-name . "ConQuR"))) + (build-system r-build-system) + (propagated-inputs (list r-ade4 + r-ape + r-compositions + r-cqrreg + r-doparallel + r-dplyr + r-fastdummies + r-glmnet + r-gplots + r-gunifrac + r-quantreg + r-randomforest + r-rocr + r-vegan)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/wdl2459/ConQuR") + (synopsis "Batch effects removal for microbiome data") + (description + "This package conducts batch effects removal from a taxa read count +table by a conditional quantile regression method. The distributional +attributes of microbiome data - zero-inflation and over-dispersion, are +simultaneously considered.") + (license license:gpl3)))) + (define-public r-p2data (let ((commit "7d4c0e17d7899f9d9b08ab2bf455abe150912f4c") (revision "1")) @@ -793,6 +868,57 @@ high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib.") (license license:lgpl2.0+)))) +(define-public r-stringendo + (let ((commit "83b8f2d82a09b33b9e895438bb523a021138be01") + (revision "1")) + (package + (name "r-stringendo") + (version (git-version "0.3.4" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vertesy/Stringendo") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1ap0nhbyd6xx0yl2vgmwk38p22yrkv4k9hw13r35z4wf343rry6v")))) + (properties `((upstream-name . "Stringendo"))) + (build-system r-build-system) + (propagated-inputs (list r-devtools r-usethis)) + (home-page "https://github.com/vertesy/Stringendo") + (synopsis "Stringendo is a string parsing library") + (description + "This package provides string parsing functionalites for generating +plotnames, filenames and paths.") + (license license:gpl3)))) + +(define-public r-readwriter + (let ((commit "71454f4aa706f5d2fbe606acd95abc14224e7058") + (revision "1")) + (package + (name "r-readwriter") + (version (git-version "0.2.9" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vertesy/ReadWriter") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0sp27smhdva2hi2x0svia2l56k8xrh7p5akn78g5b0lcvz4x3hd7")))) + (properties `((upstream-name . "ReadWriter"))) + (build-system r-build-system) + (propagated-inputs + (list r-gdata r-gtools r-openxlsx r-readr r-stringendo)) + (home-page "https://github.com/vertesy/ReadWriter") + (synopsis "Functions to read and write files conveniently") + (description + "ReadWriter is a set of R functions to read and write files +conveniently.") + (license license:gpl3)))) + (define-public r-streamgraph (let ((commit "76f7173ec89d456ace5943a512e20b1f6810bbcb") (revision "1")) @@ -1262,8 +1388,7 @@ demultiplexing step.") (list python-black python-flake8 python-poetry-core - python-pytest - python-pre-commit)) + python-pytest)) (home-page "https://github.com/JonathanShor/DoubletDetection") (synopsis "This is a package to detect doublets in single-cell RNA-seq count matrices") @@ -3846,6 +3971,80 @@ sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome.") (license license:gpl3+))) +(define-public transanno + (package + (name "transanno") + (version "0.3.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/informationsea/transanno") + ;; Corresponds to tag v0.3.0 + (commit "df49050c92644ea12d9d5c6fae2186ca436dbca3"))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1jpn7s3cnd9ybk4lmfbhj2arhf6cmrv7jp74n7n87m3a3irkaif1")) + (snippet + '(with-output-to-file "liftover-rs/build.rs" + (lambda _ + (format #true + "fn main() {~@ + println!(\"cargo:rustc-link-lib=lzma\");~@ + }~%")))))) + (build-system cargo-build-system) + (arguments + (list + #:install-source? #false ;fails + #:tests? #false ;"cargo test" ignores build.rs + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'prepare-test-files + (lambda _ + (delete-file "Cargo.lock") + (substitute* "liftover-rs/Cargo.toml" + (("anyhow = \"1\"") "anyhow = \"1.0.65\"")) + (substitute* "liftover-rs/prepare-test.sh" + (("/bin/bash") + (string-append #$(this-package-native-input "bash") + "/bin/bash"))) + (invoke "bash" "prepare-test-files.sh"))) + (add-before 'patch-cargo-checksums 'do-not-build-xz + (lambda _ + ;; Detection of liblzma (in rust-lzma-sys, pulled in by + ;; rust-hts-sys) doesn't seem to work, or perhaps it really does + ;; request a static build somewhere. + (substitute* "guix-vendor/rust-lzma-sys-0.1.17.tar.xz/build.rs" + (("if .want_static && .msvc && pkg_config::probe_library\\(\"liblzma\"\\).is_ok\\(\\)") "")))) + (add-before 'install 'chdir + (lambda _ (chdir "transanno")))) + #:cargo-inputs + `(("rust-anyhow" ,rust-anyhow-1) + ("rust-autocompress" ,rust-autocompress-0.2) + ("rust-bio" ,rust-bio-0.41) + ("rust-clap" ,rust-clap-2) + ("rust-csv" ,rust-csv-1) + ("rust-flate2" ,rust-flate2-1) + ("rust-indexmap" ,rust-indexmap-1) + ("rust-log" ,rust-log-0.4) + ("rust-nom" ,rust-nom-5) + ("rust-once-cell" ,rust-once-cell-1) + ("rust-pretty-env-logger" ,rust-pretty-env-logger-0.3) + ("rust-regex" ,rust-regex-1) + ("rust-thiserror" ,rust-thiserror-1) + ("rust-serde" ,rust-serde-1) + ("rust-serde-json" ,rust-serde-json-1)) + #:cargo-development-inputs + `(("rust-clap" ,rust-clap-2) + ("rust-lazy-static" ,rust-lazy-static-1)))) + (native-inputs (list bash)) + (home-page "https://github.com/informationsea/transanno") + (synopsis "LiftOver tool for new genome assemblies") + (description "This package provides an accurate VCF/GFF3/GTF LiftOver tool +for new genome assemblies.") + (license license:gpl3+))) + (define-public trf (package (name "trf") @@ -8219,6 +8418,43 @@ sequence.") (supported-systems '("i686-linux" "x86_64-linux")) (license license:bsd-3))) +(define-public r-ggexpress + (let ((commit "82f169385f87af328ff971195c2f64ff3c573a8a") + (revision "1")) + (package + (name "r-ggexpress") + (version (git-version "0.6.6" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vertesy/ggExpress") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "122hnw8xv33ngcd4fd7hmf817a06ih1knrxxi0cgklj1fwinm0z4")))) + (properties `((upstream-name . "ggExpress"))) + (build-system r-build-system) + (propagated-inputs (list r-cowplot + r-ggplot2 + r-ggpubr + r-markdownhelpers + r-markdownreports + r-rcolorbrewer + r-sessioninfo + r-seurat + r-sm + r-stringendo + r-tidyverse)) + (home-page "https://github.com/vertesy/ggExpress") + (synopsis + "This is a fast tool to create, annotate and export plots in R") + (description + "This package is a set of R functions for generating precise figures. +This tool helps you to create clean markdown reports about what you just +discovered with your analysis script.") + (license license:gpl3)))) + (define-public r-gg3d (let ((commit "ffdd837d30c1671cd0895db94bdd7b1594dbfcb0") (revision "1")) @@ -8535,7 +8771,10 @@ Pore-C concatemers.") r-seurat r-singlecellexperiment r-slingshot - r-summarizedexperiment)) + r-summarizedexperiment + python + python-scrublet + python-doubletdetection)) (home-page "https://github.com/xnnba1984/DoubletCollection") (synopsis "Tool for finding doublets in scRNA-seq data") (description @@ -8544,6 +8783,46 @@ doublet-detection methods. In addition, this tool is used for execution and benchmark of those eight mentioned methods.") (license license:gpl3+)))) +(define-public r-plsdabatch + (let ((commit "4aadf3a99709afae462db310386b6cf5db20088c") + (revision "1")) + (package + (name "r-plsdabatch") + (version (git-version "0.2.3" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/EvaYiwenWang/PLSDAbatch") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "047l923lq2ji7rwybh9b9zkblzvvhkpli5gb2x8g2q9f2n5022nr")))) + (properties `((upstream-name . "PLSDAbatch"))) + (build-system r-build-system) + (propagated-inputs (list r-ggplot2 + r-ggpubr + r-gridextra + r-lmertest + r-mixomics + r-mvtnorm + r-performance + r-rdpack + r-scales)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/EvaYiwenWang/PLSDAbatch") + (synopsis "PLSDA-batch") + (description + "This package provides a new batch effect correction method based on +Projection to Latent Structures Discriminant Analysis named “PLSDA-batch” to +correct data prior to any downstream analysis. PLSDA-batch estimates latent +components related to treatment and batch effects to remove batch variation. +The method is multivariate, non-parametric and performs dimension reduction. +Combined with centered log ratio transformation for addressing uneven library +sizes and compositional structure, PLSDA-batch addresses all characteristics +of microbiome data that existing correction methods have ignored so far.") + (license license:gpl3)))) + (define-public r-psupertime (let ((commit "73825a28d3bd9bc881c15ee0c4c218eec1c9c207") (revision "1")) @@ -8639,6 +8918,62 @@ target genes, Pando simultaneously infers gene modules and sets of regulatory regions for each transcription factor.") (license license:expat))) +(define-public r-premessa + (let ((commit "68b42bb984637d0f3ad6a0ecc83e9278994afc85") + (revision "1")) + (package + (name "r-premessa") + (version (git-version "0.3.4" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ParkerICI/premessa") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1l0q431zk0lvg22130nx84gdqi7cpl05yah4am63lbx6m4c769pb")) + (snippet + '(delete-file "inst/normalizer_shinyGUI/www/d3.min.js")))) + (properties `((upstream-name . "premessa"))) + (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/normalizer_shinyGUI/www/" + (invoke "esbuild" (assoc-ref inputs "d3.v4.js") + "--minify" "--outfile=d3.min.js"))))))) + (propagated-inputs + (list r-data-table + r-flowcore + r-ggplot2 + r-gridextra + r-hexbin + r-jsonlite + r-reshape + r-rhandsontable + r-shiny + r-shinyjqui)) + (native-inputs + `(("esbuild" ,esbuild) + ("d3.v4.js" + ,(origin + (method url-fetch) + (uri "https://d3js.org/d3.v4.js") + (sha256 + (base32 + "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg")))))) + (home-page "https://github.com/ParkerICI/premessa") + (synopsis "Pre-processing of flow and mass cytometry data") + (description + "This is an R package for pre-processing of flow and mass cytometry +data. This package includes panel editing or renaming for FCS files, +bead-based normalization and debarcoding.") + (license license:gpl3)))) + (define-public r-presto (let ((commit "052085db9c88aa70a28d11cc58ebc807999bf0ad") (revision "0")) @@ -8730,6 +9065,70 @@ auROC analysis.") visualization and analysis of single-cell data using R.") (license license:gpl3+)))) +(define-public r-markdownhelpers + (let ((commit "793372d28ebed607cc1d35f909a1caedb2b41ffe") + (revision "1")) + (package + (name "r-markdownhelpers") + (version (git-version "0.2.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vertesy/MarkdownHelpers") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1d18s2ydhfjm3hjkxz42dirhwrrv792m6mvkmypallaa2qnwrmkg")))) + (properties `((upstream-name . "MarkdownHelpers"))) + (build-system r-build-system) + (propagated-inputs (list r-devtools r-stringendo r-usethis)) + (home-page "https://github.com/vertesy/MarkdownHelpers") + (synopsis "Helper functions for MarkdownReports and ggExpress") + (description + "This package provides a set of R functions to parse markdown and other +generic helpers.") + (license license:gpl3)))) + +(define-public r-markdownreports + (let ((commit "3ba1103e3ddc6df3a0c090eb884f5e65c461eb31") + (revision "1")) + (package + (name "r-markdownreports") + (version (git-version "4.5.9" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vertesy/MarkdownReports") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1xmasdb630b6nvxi5m1i8pyxiy49nxpzyxf9h8spdppx92rhdkc8")))) + (properties `((upstream-name . "MarkdownReports"))) + (build-system r-build-system) + (propagated-inputs + (list r-clipr + r-codeandroll2 + r-colorramps + r-devtools + r-gplots + r-markdownhelpers + r-rcolorbrewer + r-readwriter + r-sessioninfo + r-sm + r-stringendo + r-venndiagram + r-vioplot)) + (home-page "https://github.com/vertesy/MarkdownReports") + (synopsis "Tool for generating cientific figures and reports") + (description + "This is a set of R functions that allows you to generate precise +figures. This tool will create clean markdown reports about what you just +discovered.") + (license license:gpl3)))) + (define-public r-snapatac (package (name "r-snapatac") @@ -8779,6 +9178,30 @@ clustering analysis, differential analysis, motif inference and exploration of single cell ATAC-seq sequencing data.") (license license:gpl3))) +(define-public r-tictoc + (package + (name "r-tictoc") + (version "1.1") + (source (origin + (method url-fetch) + (uri (cran-uri "tictoc" version)) + (sha256 + (base32 + "0ka7zd857xfqb5afn0psn0yzfv2qjb0ddxfyiq6aggbnla5qc3qj")))) + (properties `((upstream-name . "tictoc"))) + (build-system r-build-system) + (home-page "https://github.com/jabiru/tictoc") + (synopsis + "Time R scripts and implementations of stack and list structures") + (description + "The tictoc package provides the timing functions @code{tic} and +@code{toc} that can be nested. It provides an alternative to +@code{system.time()} with a different syntax similar to that in another +well-known software package. @code{tic} and @code{toc} are easy to use, and +are especially useful when timing several sections in more than a few lines of +code.") + (license license:asl2.0))) + (define-public r-tsis (let ((commit "24460298fbe1d26e4da390f6e4f3d4d9d62334dc") (revision "1")) @@ -15729,6 +16152,60 @@ information... The package can also be used to extract data from @code{.loom} files.") (license license:expat)))) +(define-public r-seurat-utils + (let ((commit "0b6f5b548a49148cfbeaa654e8a618c0a020afa5") + (revision "1")) + (package + (name "r-seurat-utils") + (version (git-version "1.6.5" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vertesy/Seurat.utils") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1mn64h375mkj6x4ix5493z32gqg96yc507j5jr0lx9g5wk1bf762")))) + (properties `((upstream-name . "Seurat.utils"))) + (build-system r-build-system) + (propagated-inputs (list r-codeandroll2 + r-cowplot + r-dplyr + r-ggcorrplot + r-ggexpress + r-ggplot2 + r-ggpubr + r-ggrepel + r-hgnchelper + r-htmlwidgets + r-markdownhelpers + r-markdownreports + r-matrix + r-matrixstats + r-princurve + r-r-utils + r-readr + r-readwriter + r-reshape2 + r-scales + r-seurat + r-soupx + r-sparsematrixstats + r-stringendo + r-stringr + r-tibble + r-tictoc + r-vroom)) + (home-page "https://github.com/vertesy/Seurat.utils") + (synopsis "Collection of utility functions for Seurat") + (description + "This is a collection of utility functions for Seurat. These functions +allow the automation and multiplexing of plotting, 3D plotting, visualization +of statistics & QC, interaction with the Seurat object. Some functionalities +require functions from CodeAndRoll and MarkdownReports libraries.") + (license license:gpl3)))) + (define-public r-seuratwrappers ;; There are no releases or tags. (let ((commit "d28512f804d5fe05e6d68900ca9221020d52cf1d") @@ -17846,7 +18323,6 @@ aligner.") (list python-black python-flake8 python-hypothesis - python-pre-commit python-pytest python-setuptools-scm python-wheel)) |