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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.


starlong 2.7.8a
Dependencies: htslib@1.21 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/alexdobin/STAR
Licenses: GPL 3+
Build system: gnu
Synopsis: Universal RNA-seq aligner
Description:

The Spliced Transcripts Alignment to a Reference (STAR) software is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences.

aragorn 1.2.41
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.ansikte.se/ARAGORN/
Licenses: GPL 3+
Build system: gnu
Synopsis: Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences
Description:

Aragorn identifies transfer RNA, mitochondrial RNA and transfer-messenger RNA from nucleotide sequences, based on homology to known tRNA consensus sequences and RNA structure. It also outputs the secondary structure of the predicted RNA.

python-genomepy 0.15.0
Propagated dependencies: python-appdirs@1.4.4 python-biopython@1.85 python-click@8.1.8 python-colorama@0.4.6 python-diskcache@5.6.3 python-filelock@3.16.1 python-loguru@0.7.2 python-mygene@3.2.2 python-mysql-connector-python@8.0.33 python-norns@0.1.6 python-numpy@1.26.4 python-pandas@2.2.3 python-pyfaidx@0.7.2.1 python-requests@2.32.5 python-tqdm@4.67.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://vanheeringen-lab.github.io/genomepy/
Licenses: Expat
Build system: pyproject
Synopsis: Genes and genomes at your fingertips
Description:

genomepy is designed to provide a simple and straightforward way to download and use genomic data. This includes

  1. searching available data,

  2. showing the available metadata,

  3. automatically downloading, preprocessing and matching data, and

  4. generating optional aligner indexes.

All with sensible, yet controllable defaults.

r-metacell 0.3.41-1.d6a6926
Propagated dependencies: r-cluster@2.1.8.1 r-cowplot@1.2.0 r-data-table@1.17.8 r-dbscan@1.2.3 r-domc@1.3.8 r-dplyr@1.1.4 r-entropy@1.3.2 r-ggplot2@4.0.1 r-graph@1.88.0 r-igraph@2.2.1 r-kernsmooth@2.23-26 r-magrittr@2.0.4 r-matrix@1.7-4 r-matrixstats@1.5.0 r-pdist@1.2.1 r-pheatmap@1.0.13 r-plyr@1.8.9 r-rcolorbrewer@1.1-3 r-rcurl@1.98-1.17 r-rgraphviz@2.54.0 r-slam@0.1-55 r-singlecellexperiment@1.32.0 r-svglite@2.2.2 r-tgconfig@0.1.2-1.15cf199 r-tgstat@2.3.29 r-tgutil@0.1.15-1.db4ff8b r-tidyr@1.3.1 r-umap@0.2.10.0 r-umap@0.2.10.0 r-zoo@1.8-14
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/tanaylab/metacell/
Licenses: Expat
Build system: r
Synopsis: Meta cell analysis for single cell RNA-seq data
Description:

This package facilitates the analysis of single-cell RNA-seq UMI matrices. It does this by computing partitions of a cell similarity graph into small homogeneous groups of cells, which are defined as metacells (MCs). The derived MCs are then used for building different representations of the data, allowing matrix or 2D graph visualization forming a basis for analysis of cell types, subtypes, transcriptional gradients,cell-cycle variation, gene modules and their regulatory models and more.

scallop 0.10.5
Dependencies: boost@1.89.0 htslib@1.21
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/Kingsford-Group/scallop
Licenses: Modified BSD
Build system: gnu
Synopsis: Reference-based transcriptome assembler for RNA-seq
Description:

Scallop is a reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts.

python-demuxem 0.1.7
Propagated dependencies: python-docopt@0.6.2 python-importlib-metadata@8.7.0 python-numpy@1.26.4 python-pandas@2.2.3 python-pegasusio@0.9.1 python-scikit-learn@1.7.0 python-scipy@1.12.0 python-seaborn@0.13.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/lilab-bcb/demuxEM
Licenses: Modified BSD
Build system: pyproject
Synopsis: Analyze cell-hashing/nucleus-hashing data
Description:

This is a Python module for analyzing cell-hashing/nucleus-hashing data. It is the demultiplexing module of Pegasus, which is used by Cumulus in the demultiplexing step.

pigx-sars-cov2-ww 0.0.9
Dependencies: bash-minimal@5.2.37 bedtools@2.31.1 bwa@0.7.18 ensembl-vep@112 fastp@0.23.2 fastqc@0.11.9 ivar@1.4.4 kraken2@2.1.2 krona-tools@2.8 lofreq@2.1.5 multiqc@1.14 python-pyyaml@6.0.2 python-wrapper@3.11.14 r-base64url@1.4 r-data-table@1.17.8 r-deconvr@1.16.0 r-dplyr@1.1.4 r-dt@0.34.0 r-ggplot2@4.0.1 r-htmltools@0.5.8.1 r-jsonlite@2.0.0 r-knitr@1.50 r-magrittr@2.0.4 r-mass@7.3-65 r-minimal@4.5.2 r-plotly@4.11.0 r-qpcr@1.4-2 r-r-utils@2.13.0 r-reshape2@1.4.5 r-rmarkdown@2.30 r-stringr@1.6.0 r-tidyr@1.3.1 r-viridis@0.6.5 samtools@1.19 snakemake@7.32.4 wget@1.25.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://bioinformatics.mdc-berlin.de/pigx/
Licenses: GPL 3+
Build system: gnu
Synopsis: Analysis pipeline for wastewater sequencing
Description:

PiGx SARS-CoV-2 is a pipeline for analysing data from sequenced wastewater samples and identifying given variants-of-concern of SARS-CoV-2. The pipeline can be used for continuous sampling. The output report will provide an intuitive visual overview about the development of variant abundance over time and location.

r-xbioc 0.1.16-1.6ff0670
Propagated dependencies: r-annotationdbi@1.72.0 r-assertthat@0.2.1 r-biobase@2.70.0 r-biocmanager@1.30.27 r-digest@0.6.39 r-pkgmaker@0.32.10 r-plyr@1.8.9 r-reshape2@1.4.5 r-stringr@1.6.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/renozao/xbioc/
Licenses: GPL 3+
Build system: r
Synopsis: Extra base functions for Bioconductor
Description:

This package provides extra utility functions to perform common tasks in the analysis of omics data, leveraging and enhancing features provided by Bioconductor packages.

imp 2.23.0
Dependencies: boost@1.59.0 cereal@1.3.2 cgal@5.6.1 gsl@2.8 hdf5@1.14.6 fftw@3.3.10 eigen@3.4.0 opencv@4.12.0
Propagated dependencies: python-numpy@1.26.4 python-scipy@1.12.0 python-pandas@2.2.3 python-scikit-learn@1.7.0 python-networkx@3.4.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://integrativemodeling.org
Licenses: LGPL 2.1+ GPL 3+
Build system: cmake
Synopsis: Integrative modeling platform
Description:

IMP's broad goal is to contribute to a comprehensive structural characterization of biomolecules ranging in size and complexity from small peptides to large macromolecular assemblies, by integrating data from diverse biochemical and biophysical experiments. IMP provides a C++ and Python toolbox for solving complex modeling problems, and a number of applications for tackling some common problems in a user-friendly way.

python-cyvcf2 0.31.2
Dependencies: curl@8.6.0 htslib@1.21 libdeflate@1.19 openssl@3.0.8 zlib@1.3.1
Propagated dependencies: python-click@8.1.8 python-coloredlogs@10.0 python-numpy@1.26.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/brentp/cyvcf2/
Licenses: Expat
Build system: pyproject
Synopsis: Fast vcf file parsing with Cython and htslib
Description:

Cyvcf2 is a Cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files.

freebayes 1.3.9
Dependencies: bzip2@1.0.8 fastahack@1.0.0 htslib@1.21 smithwaterman@0.0.0-2.2610e25 tabixpp@1.1.2 vcflib@1.0.12 xz@5.4.5
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/freebayes/freebayes
Licenses: Expat
Build system: meson
Synopsis: Haplotype-based variant detector
Description:

FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.

ciri-long 1.0.2
Dependencies: circtools@1.0.0 python-biopython@1.85 python-bwapy@0.1.4 python-levenshtein@0.27.1 python-mappy@2.24 python-numpy@1.26.4 python-pandas@2.2.3 python-pysam@0.23.0 python-pyspoa@0.0.5 python-scikit-learn@1.7.0 python-scipy@1.12.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://ciri-cookbook.readthedocs.io/
Licenses: Expat
Build system: pyproject
Synopsis: Circular RNA identification for Nanopore sequencing
Description:

CIRI-long is a package for circular RNA identification using long-read sequencing data.

rseqc 3.0.1
Dependencies: python-bx-python@0.14.0 python-cython@3.1.2 python-numpy@1.26.4 python-pybigwig@0.3.22 python-pyparsing@3.2.3 python-pysam@0.23.0 python-setuptools@80.9.0 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://rseqc.sourceforge.net/
Licenses: GPL 3+
Build system: pyproject
Synopsis: RNA-seq quality control package
Description:

RSeQC provides a number of modules that can comprehensively evaluate high throughput sequence data, especially RNA-seq data. Some basic modules inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, etc.

ribotaper 1.3.1
Dependencies: bash-minimal@5.2.37 bedtools@2.18.0 samtools@0.1.19 r-minimal@4.5.2 r-foreach@1.5.2 r-xnomial@1.0.4.1 r-domc@1.3.8 r-multitaper@1.0-17 r-seqinr@4.2-36
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/
Licenses: GPL 3+
Build system: gnu
Synopsis: Define translated ORFs using ribosome profiling data
Description:

Ribotaper is a method for defining translated open reading frames (ORFs) using ribosome profiling (ribo-seq) data. This package provides the Ribotaper pipeline.

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
Build system: ruby
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.

metal 2011-03-25
Dependencies: zlib@1.3.1 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://csg.sph.umich.edu/abecasis/Metal/
Licenses: Modified BSD
Build system: gnu
Synopsis: Facilitate meta-analysis of large datasets
Description:

METAL is a tool for meta-analysis genomewide association scans. METAL can combine either test statistics and standard errors or p-values across studies (taking sample size and direction of effect into account). METAL analysis is a convenient alternative to a direct analysis of merged data from multiple studies. It is especially appropriate when data from the individual studies cannot be analyzed together because of differences in ethnicity, phenotype distribution, gender or constraints in sharing of individual level data imposed. Meta-analysis results in little or no loss of efficiency compared to analysis of a combined dataset including data from all individual studies.

prinseq 0.20.4
Dependencies: guile@3.0.9 perl@5.36.0 perl-cairo@1.109 perl-data-dumper@2.183 perl-digest-md5@2.58 perl-getopt-long@2.51 perl-json@4.02 perl-statistics-pca@0.0.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://prinseq.sourceforge.net/
Licenses: GPL 3+
Build system: gnu
Synopsis: Preprocess sequence data in FASTA or FASTQ formats
Description:

PRINSEQ is a bioinformatics tool to help you preprocess your genomic or metagenomic sequence data in FASTA or FASTQ formats. The tool is written in Perl and can be helpful if you want to filter, reformat, or trim your sequence data. It also generates basic statistics for your sequences.

dropseq-tools 1.13
Dependencies: icedtea@3.19.0 java-picard@2.10.3 java-log4j-1.2-api@2.17.1 java-commons-math3@3.6.1 java-commons-jexl@2.1.1 java-commons-collections4@4.1 java-commons-lang@2.6 java-commons-io@2.5 java-snappy@1.0.3-rc3 java-guava@31.1 java-la4j@0.6.0 java-biojava-core@4.0.0 java-biojava-alignment@4.0.0 java-jdistlib@0.4.5 java-simple-xml@2.7.1 java-snakeyaml@1.18
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://mccarrolllab.com/dropseq/
Licenses: Expat
Build system: ant
Synopsis: Tools for Drop-seq analyses
Description:

Drop-seq is a technology to enable biologists to analyze RNA expression genome-wide in thousands of individual cells at once. This package provides tools to perform Drop-seq analyses.

python-biom-format 2.1.16
Propagated dependencies: python-anndata@0.12.1 python-click@8.1.8 python-flake8@7.1.1 python-future@1.0.0 python-h5py@3.13.0 python-numpy@1.26.4 python-pandas@2.2.3 python-scipy@1.12.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.biom-format.org
Licenses: Modified BSD
Build system: pyproject
Synopsis: Biological Observation Matrix (BIOM) format utilities
Description:

The BIOM file format is designed to be a general-use format for representing counts of observations e.g. operational taxonomic units, KEGG orthology groups or lipid types, in one or more biological samples e.g. microbiome samples, genomes, metagenomes.

gffcompare 0.10.15-1.be56ef4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/gpertea/gffcompare/
Licenses: Expat Artistic License 2.0
Build system: gnu
Synopsis: Tool for comparing or classifing transcripts of RNA-Seq
Description:

gffcompare is a tool that can:

  1. compare and evaluate the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie);

  2. collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g. resulted from assembly of different samples);

  3. classify transcripts from one or multiple GTF/GFF3 files as they relate to reference transcripts provided in a annotation file (also in GTF/GFF3 format).

r-compgenomrdata 0.1.0-1.24484cb
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/compgenomr/compGenomRData
Licenses: GPL 3
Build system: r
Synopsis: Data for Computational Genomics with R book
Description:

This package provides data for the book "Computational Genomics with R".

pbgzip 0.0.0-0.2b09f97
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/nh13/pbgzip
Licenses: Expat
Build system: gnu
Synopsis: Parallel Block GZIP
Description:

This package implements parallel block gzip. For many formats, in particular genomics data formats, data are compressed in fixed-length blocks such that they can be easily indexed based on a (genomic) coordinate order, since typically each block is sorted according to this order. This allows for each block to be individually compressed (deflated), or more importantly, decompressed (inflated), with the latter enabling random retrieval of data in large files (gigabytes to terabytes). pbgzip is not limited to any particular format, but certain features are tailored to genomics data formats when enabled. Parallel decompression is somewhat faster, but the true speedup comes during compression.

r-centipede 1.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://centipede.uchicago.edu/
Licenses: GPL 2+ GPL 3+
Build system: r
Synopsis: Predict transcription factor binding sites
Description:

CENTIPEDE applies a hierarchical Bayesian mixture model to infer regions of the genome that are bound by particular transcription factors. It starts by identifying a set of candidate binding sites, and then aims to classify the sites according to whether each site is bound or not bound by a transcription factor. CENTIPEDE is an unsupervised learning algorithm that discriminates between two different types of motif instances using as much relevant information as possible.

python-cwl-utils 0.32
Dependencies: node@22.14.0
Propagated dependencies: python-cwl-upgrader@1.2.11 python-cwlformat@2022.02.18 python-packaging@25.0 python-rdflib@7.1.1 python-requests@2.32.5 python-ruamel.yaml@0.18.14 python-schema-salad@8.9.20250723145140
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/common-workflow-language/cwl-utils
Licenses: ASL 2.0
Build system: pyproject
Synopsis: Python utilities for CWL
Description:

python-cwl-utils provides python utilities and autogenerated classes for loading and parsing CWL v1.0, CWL v1.1, and CWL v1.2 documents.

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