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      /\__ \     / /\ \ \\ \ \_/ / /     / / /\ \__
     / /_ \ \   / / /\ \ \\ \___/ /     / / /\ \___\
    / / /\ \ \ / / /  \ \_\\ \ \_/      \ \ \ \/___/
   / / /  \/_// / /   / / / \ \ \        \ \ \
  / / /      / / /   / / /   \ \ \   _    \ \ \
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/_/ /      / / /____\/ /       \ \_\\ \/___/ /
\_\/       \/_________/         \/_/ \_____\/

Enter the query into the form above. You can look for specific version of a package by using @ symbol like this: gcc@10.

API method:

GET /api/packages?search=hello&page=1&limit=20

where search is your query, page is a page number and limit is a number of items on a single page. Pagination information (such as a number of pages and etc) is returned in response headers.

If you'd like to join our channel webring send a patch to ~whereiseveryone/toys@lists.sr.ht adding your channel as an entry in channels.scm.


python-bcbio-gff 0.7.1
Propagated dependencies: python-biopython@1.73 python-six@1.17.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/chapmanb/bcbb/tree/master/gff
Licenses: non-copyleft
Synopsis: Read and write GFF files with Biopython integration
Description:

This package lets you read and write files in Generic Feature Format (GFF) with Biopython integration.

r-stringendo 0.6.0-1.15594b1
Propagated dependencies: r-clipr@0.8.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/vertesy/Stringendo
Licenses: GPL 3
Synopsis: Stringendo is a string parsing library
Description:

This package provides string parsing functionalities for generating plotnames, filenames and paths.

pigx-rnaseq 0.1.1
Dependencies: coreutils@9.1 sed@4.9 gzip@1.14 snakemake@7.32.4 megadepth@1.1.1 multiqc@1.14 star@2.7.3a hisat2@2.2.1 fastp@0.23.2 htseq@2.0.2 samtools@1.19 r-minimal@4.5.0 r-rmarkdown@2.29 r-ggplot2@3.5.2 r-ggpubr@0.6.0 r-ggrepel@0.9.6 r-gprofiler2@0.2.3 r-deseq2@1.48.1 r-dt@0.33 r-knitr@1.50 r-pheatmap@1.0.12 r-corrplot@0.95 r-reshape2@1.4.4 r-plotly@4.10.4 r-scales@1.4.0 r-summarizedexperiment@1.38.1 r-crosstalk@1.2.1 r-tximport@1.36.0 r-rtracklayer@1.68.0 r-rjson@0.2.23 salmon@1.10.3 pandoc@2.19.2 python-wrapper@3.11.11 python-deeptools@3.5.5 python-pyyaml@6.0.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://bioinformatics.mdc-berlin.de/pigx/
Licenses: GPL 3+
Synopsis: Analysis pipeline for RNA sequencing experiments
Description:

PiGX RNAseq is an analysis pipeline for preprocessing and reporting for RNA sequencing experiments. It is easy to use and produces high quality reports. The inputs are reads files from the sequencing experiment, and a configuration file which describes the experiment. In addition to quality control of the experiment, the pipeline produces a differential expression report comparing samples in an easily configurable manner.

orfm 0.7.1
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/wwood/OrfM
Licenses: LGPL 3+
Synopsis: Simple and not slow open reading frame (ORF) caller
Description:

An ORF caller finds stretches of DNA that, when translated, are not interrupted by stop codons. OrfM finds and prints these ORFs.

shorah 1.99.2
Dependencies: bash-minimal@5.2.37 boost@1.83.0 htslib@1.21 python@3.11.11 python-biopython@1.85 python-numpy@1.26.4 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page:
Licenses: GPL 3+
Synopsis: Short reads assembly into haplotypes
Description:

ShoRAH is a project for the analysis of next generation sequencing data. It is designed to analyse genetically heterogeneous samples. Its tools provide error correction, haplotype reconstruction and estimation of the frequency of the different genetic variants present in a mixed sample.

r-scde 1.99.2
Propagated dependencies: r-rcpp@1.0.14 r-rcpparmadillo@14.4.3-1 r-mgcv@1.9-3 r-rook@1.2 r-rjson@0.2.23 r-cairo@1.6-2 r-rcolorbrewer@1.1-3 r-edger@4.6.2 r-quantreg@6.1 r-nnet@7.3-20 r-rmtstat@0.3.1 r-extremes@2.2-1 r-pcamethods@2.0.0 r-biocparallel@1.42.0 r-flexmix@2.3-20
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://hms-dbmi.github.io/scde/
Licenses: GPL 2
Synopsis: R package for analyzing single-cell RNA-seq data
Description:

The SCDE package implements a set of statistical methods for analyzing single-cell RNA-seq data. SCDE fits individual error models for single-cell RNA-seq measurements. These models can then be used for assessment of differential expression between groups of cells, as well as other types of analysis. The SCDE package also contains the pagoda framework which applies pathway and gene set overdispersion analysis to identify aspects of transcriptional heterogeneity among single cells.

hh-suite 3.3.0
Dependencies: openmpi@4.1.6 simde@0.8.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3019-7
Licenses: GPL 3+
Synopsis: Remote protein homology detection suite
Description:

The HH-suite is a software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).

r-gg3d 0.0.0.9000-1.ffdd837
Propagated dependencies: r-dplyr@1.1.4 r-ggplot2@3.5.2 r-magrittr@2.0.3 r-plot3d@1.4.1 r-plyr@1.8.9 r-scales@1.4.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/AckerDWM/gg3D
Licenses: GPL 3+
Synopsis: 3D perspective plots for ggplot2
Description:

This package adds 3D perspective plotting of points, paths, and line, 3D perspective axes, 3D perspective annotations, and wireframe plots.

python-iced 0.5.13
Propagated dependencies: python-numpy@1.26.4 python-pandas@2.2.3 python-scipy@1.12.0 python-scikit-learn@1.7.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/hiclib/iced
Licenses: Modified BSD
Synopsis: ICE normalization
Description:

This is a package for normalizing Hi-C contact counts efficiently.

python-readpaf 0.0.10
Propagated dependencies: python-pandas@2.2.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/alexomics/read-paf
Licenses: Expat
Synopsis: Minimap2 PAF file reader
Description:

This is a fast parser for minimap2 PAF (Pairwise mApping Format) files.

r-singlet 0.99.26-1.765a6c4
Propagated dependencies: r-dplyr@1.1.4 r-fgsea@1.34.0 r-ggplot2@3.5.2 r-knitr@1.50 r-limma@3.64.1 r-matrix@1.7-3 r-msigdbr@24.1.0 r-rcpp@1.0.14 r-rcppml-devel@0.5.6-2.5449a5b r-reshape2@1.4.4 r-scuttle@1.18.0 r-seurat@5.3.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/zdebruine/singlet
Licenses: GPL 2+
Synopsis: Non-negative Matrix Factorization for single-cell analysis
Description:

This is a package for fast Non-negative Matrix Factorization (NMF) with automatic rank-determination for dimension reduction of single-cell data using Seurat, RcppML nmf, SingleCellExperiments and similar.

r-scenic 1.3.1-1.cedf849
Propagated dependencies: r-aucell@1.30.1 r-data-table@1.17.4 r-dynamictreecut@1.63-1 r-genie3@1.30.0 r-ggrepel@0.9.6 r-mixtools@2.0.0.1 r-nmf@0.28 r-rcistarget@1.28.1 r-rtsne@0.17
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/aertslab/SCENIC
Licenses: GPL 3
Synopsis: SCENIC (Single Cell rEgulatory Network Inference and Clustering)
Description:

SCENIC (Single-cell regulatory network inference and clustering) is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

lofreq 2.1.5
Dependencies: htslib@1.21 python-wrapper@3.11.11 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://csb5.github.io/lofreq/
Licenses: Expat
Synopsis: Sensitive variant calling from sequencing data
Description:

LoFreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.

transanno 0.4.5
Dependencies: xz@5.4.5 zstd@1.5.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/informationsea/transanno
Licenses: GPL 3+
Synopsis: LiftOver tool for new genome assemblies
Description:

This package provides an accurate VCF/GFF3/GTF LiftOver tool for new genome assemblies.

umi-tools 1.1.6
Dependencies: python-pandas@2.2.3 python-future@1.0.0 python-scipy@1.12.0 python-matplotlib@3.8.2 python-regex@2024.11.6 python-pybktree@1.1 python-scipy@1.12.0 python-pysam@0.23.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/CGATOxford/UMI-tools
Licenses: Expat
Synopsis: Tools for analyzing unique modular identifiers
Description:

This package provides tools for dealing with Unique Molecular Identifiers (UMIs) and Random Molecular Tags (RMTs) in genetic sequences. There are six tools: the extract and whitelist commands are used to prepare a fastq containing UMIs +/- cell barcodes for alignment. The remaining commands, group, dedup, and count/count_tab, are used to identify PCR duplicates using the UMIs and perform different levels of analysis depending on the needs of the user.

python-twobitreader 3.1.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/benjschiller/twobitreader
Licenses: Artistic License 2.0
Synopsis: Python library for reading .2bit files
Description:

twobitreader is a Python library for reading .2bit files as used by the UCSC genome browser.

bioawk 1.0
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/lh3/bioawk
Licenses: X11
Synopsis: AWK with bioinformatics extensions
Description:

Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few built-in functions and a command line option to use TAB as the input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk.

bpp-popgen 2.4.1
Dependencies: bpp-core@2.4.1 bpp-seq@2.4.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://pbil.univ-lyon1.fr/bpp-doc/bpp-popgen/html/
Licenses: CeCILL-C
Synopsis: Bio++ population genetics library
Description:

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. This library provides population genetics-related modules.

r-rhtslib12 1.23.2-1.ee186da
Propagated dependencies: curl@8.6.0 zlib@1.3.1 r-zlibbioc@1.54.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/haizi-zh/Rhtslib12
Licenses: LGPL 2.0+
Synopsis: HTSlib high-throughput sequencing library as an R package
Description:

This package provides version 1.12 of the HTSlib C library for high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib.

bwa-pssm 0.5.11
Dependencies: gdsl@1.8 zlib@1.3.1 perl@5.36.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/pkerpedjiev/bwa-pssm
Licenses: GPL 3+
Synopsis: Burrows-Wheeler transform-based probabilistic short read mapper
Description:

BWA-PSSM is a probabilistic short genomic sequence read aligner based on the use of position specific scoring matrices (PSSM). Like many of the existing aligners it is fast and sensitive. Unlike most other aligners, however, it is also adaptible in the sense that one can direct the alignment based on known biases within the data set. It is coded as a modification of the original BWA alignment program and shares the genome index structure as well as many of the command line options.

libsbml 5.20.5
Propagated dependencies: libxml2@2.14.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://sbml.org/Software/libSBML
Licenses: LGPL 2.1+
Synopsis: Process SBML files and data streams
Description:

LibSBML is a library to help you read, write, manipulate, translate, and validate SBML files and data streams. The Systems Biology Markup Language (SBML) is an interchange format for computer models of biological processes. SBML is useful for models of metabolism, cell signaling, and more. It continues to be evolved and expanded by an international community.

python-pybedtools 0.10.0
Dependencies: zlib@1.3.1
Propagated dependencies: bedtools@2.31.1 samtools@1.19 kentutils@302.0.0 python-numpy@1.26.4 python-pandas@2.2.3 python-psutil@7.0.0 python-pysam@0.23.0 python-pyyaml@6.0.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://pythonhosted.org/pybedtools/
Licenses: Expat LGPL 2.1+
Synopsis: Python wrapper for BEDtools programs
Description:

This package is a Python wrapper for Aaron Quinlan's BEDtools programs, which are widely used for genomic interval manipulation or "genome algebra". pybedtools extends BEDTools by offering feature-level manipulations from with Python.

ruby-bio-kseq 0.0.2
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/gusevfe/bio-kseq
Licenses: Expat
Synopsis: Ruby bindings for the kseq.h FASTA/Q parser
Description:

Bio::Kseq provides ruby bindings to the kseq.h FASTA and FASTQ parsing code. It provides a fast iterator over sequences and their quality scores.

r-vitesscer 0.99.0-1.0096880
Propagated dependencies: r-delayedarray@0.34.1 r-future@1.49.0 r-htmlwidgets@1.6.4 r-httpuv@1.6.16 r-jsonlite@2.0.0 r-matrix@1.7-3 r-mime@0.13 r-plumber@1.3.0 r-r6@2.6.1 r-s4vectors@0.46.0 r-stringi@1.8.7 r-stringr@1.5.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/vitessce/vitessceR
Licenses: Expat
Synopsis: Create interactive Single-cell visualizations
Description:

This package provides an R API and htmlwidget facilitating interactive visualization of spatial single-cell data with Vitessce. The R API contains classes and functions for loading single-cell data stored in compatible on-disk formats. The htmlwidget is a wrapper around the Vitessce JavaScript library and can be used in the Viewer tab of RStudio or Shiny apps.

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