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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.


clipper-peak 2.0.1
Dependencies: htseq@2.0.2 python-pybedtools@0.10.0 python-cython@3.1.2 python-scikit-learn@1.7.0 python-matplotlib@3.8.2 python-pandas@2.2.3 python-pysam@0.23.0 python-numpy@1.26.4 python-scipy@1.12.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/YeoLab/clipper
Licenses: GPL 2
Synopsis: CLIP peak enrichment recognition
Description:

CLIPper is a tool to define peaks in CLIP-seq datasets.

r-readwriter 1.5.3-1.91373c4
Propagated dependencies: r-gtools@3.9.5 r-openxlsx@4.2.8 r-readr@2.1.5 r-stringendo@0.6.0-1.15594b1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/vertesy/ReadWriter
Licenses: GPL 3
Synopsis: Functions to read and write files conveniently
Description:

ReadWriter is a set of R functions to read and write files conveniently.

r-demultiplex 1.0.2-1.6e2a142
Propagated dependencies: r-kernsmooth@2.23-26 r-reshape2@1.4.4 r-rtsne@0.17 r-shortread@1.66.0 r-stringdist@0.9.15
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/chris-mcginnis-ucsf/MULTI-seq
Licenses: CC0
Synopsis: MULTI-seq pre-processing and classification tools
Description:

deMULTIplex is an R package for analyzing single-cell RNA sequencing data generated with the MULTI-seq sample multiplexing method. The package includes software to

  1. Convert raw MULTI-seq sample barcode library FASTQs into a sample barcode UMI count matrix, and

  2. Classify cell barcodes into sample barcode groups.

codingquarry 2.0
Dependencies: openmpi@4.1.6 python2@2.7.18
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://sourceforge.net/projects/codingquarry/
Licenses: GPL 3+
Synopsis: Fungal gene predictor
Description:

CodingQuarry is a highly accurate, self-training GHMM fungal gene predictor designed to work with assembled, aligned RNA-seq transcripts.

seqan 2.4.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.seqan.de
Licenses: Modified BSD
Synopsis: Library for nucleotide sequence analysis
Description:

SeqAn is a C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. It contains algorithms and data structures for string representation and their manipulation, online and indexed string search, efficient I/O of bioinformatics file formats, sequence alignment, and more.

samtools 0.1.19
Dependencies: htslib@1.21 ncurses@6.2.20210619 perl@5.36.0 python@3.11.11 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://samtools.sourceforge.net
Licenses: Expat
Synopsis: Utilities to efficiently manipulate nucleotide sequence alignments
Description:

Samtools implements various utilities for post-processing nucleotide sequence alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer.

python-cell2cell 0.7.4
Propagated dependencies: python-gseapy@1.0.4 python-kneed@0.8.5 python-matplotlib@3.8.2 python-networkx@3.4.2 python-numpy@1.26.4 python-openpyxl@3.1.5 python-pandas@2.2.3 python-scikit-learn@1.7.0 python-scipy@1.12.0 python-seaborn@0.13.2 python-statsmodels@0.14.4 python-scanpy@1.11.2 python-seaborn@0.13.2 python-tensorly@0.9.0 python-tqdm@4.67.1 python-umap-learn@0.5.9 python-xlrd@2.0.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/earmingol/cell2cell
Licenses: Modified BSD
Synopsis: Python library for cell communication analysis
Description:

Cell2cell is a Python library for cell communication analysis. This is a method to calculate, visualize and analyze communication between cell types. Cell2cell is suitable for single-cell RNA sequencing (scRNA-seq) data.

python-ont-fast5-api 4.1.3
Dependencies: vbz-compression@1.0.13
Propagated dependencies: python-numpy@1.26.4 python-h5py@3.13.0 python-packaging@25.0 python-progressbar33@2.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/nanoporetech/ont_fast5_api
Licenses: MPL 2.0
Synopsis: Interface to HDF5 files of the Oxford Nanopore fast5 file format
Description:

This package provides a concrete implementation of the fast5 file schema using the generic h5py library, plain-named methods to interact with and reflect the fast5 file schema, and tools to convert between multi_read and single_read formats.

python-schema-salad 8.9.20250723145140
Propagated dependencies: python-cachecontrol@0.14.1 python-mistune@3.1.3 python-mypy-extensions@1.1.0 python-rdflib@7.1.1 python-requests@2.32.5 python-ruamel.yaml@0.18.14
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/common-workflow-language/schema_salad
Licenses: ASL 2.0
Synopsis: Schema Annotations for Linked Avro Data (SALAD)
Description:

Salad is a schema language for describing JSON or YAML structured linked data documents. Salad schema describes rules for preprocessing, structural validation, and hyperlink checking for documents described by a Salad schema. Salad supports rich data modeling with inheritance, template specialization, object identifiers, object references, documentation generation, code generation, and transformation to RDF. Salad provides a bridge between document and record oriented data modeling and the Semantic Web.

ncbi-vdb 2.10.6
Dependencies: file@5.46 hdf5@1.10.9 java-ngs@2.10.5 libxml2@2.14.6 ngs-sdk@2.10.5
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ncbi/ncbi-vdb
Licenses: Public Domain
Synopsis: Database engine for genetic information
Description:

The NCBI-VDB library implements a highly compressed columnar data warehousing engine that is most often used to store genetic information. Databases are stored in a portable image within the file system, and can be accessed/downloaded on demand across HTTP.

java-maxent 3.4.4
Dependencies: java-classpathx-servletapi@3.0.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://biodiversityinformatics.amnh.org/open_source/maxent
Licenses: Expat
Synopsis: Model species geographic distributions
Description:

Maxent is a stand-alone Java application for modelling species geographic distributions.

r-seuratextenddata 0.2.1-1.e7f17d4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/huayc09/SeuratExtendData
Licenses: GPL 3+
Synopsis: Data attached to SeuratExtend package
Description:

This package provides data for the SeuratExtend tool.

r-chipkernels 1.1-1.c9cfcac
Propagated dependencies: r-iranges@2.42.0 r-xvector@0.48.0 r-biostrings@2.76.0 r-bsgenome@1.76.0 r-gtools@3.9.5 r-genomicranges@1.60.0 r-sfsmisc@1.1-20 r-kernlab@0.9-33 r-s4vectors@0.46.0 r-biocgenerics@0.54.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ManuSetty/ChIPKernels
Licenses: GPL 2+
Synopsis: Build string kernels for DNA Sequence analysis
Description:

ChIPKernels is an R package for building different string kernels used for DNA Sequence analysis. A dictionary of the desired kernel must be built and this dictionary can be used for determining kernels for DNA Sequences.

python-airr 1.5.1
Propagated dependencies: python-pandas@2.2.3 python-pyyaml@6.0.2 python-yamlordereddictloader@0.4.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://docs.airr-community.org
Licenses: CC-BY 4.0
Synopsis: Data Representation Standard library for antibody and TCR sequences
Description:

Python-airr provides a library by the AIRR community to for describing, reporting, storing, and sharing adaptive immune receptor repertoire (AIRR) data, such as sequences of antibodies and T cell receptors (TCRs).

r-umi4cpackage 0.0.1-1.88b07d8
Dependencies: perl@5.36.0 bowtie@2.3.4.3
Propagated dependencies: r-misha@4.1.0 r-zoo@1.8-14
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/tanaylab/umi4cpackage
Licenses: Expat
Synopsis: Processing and analysis of UMI-4C contact profiles
Description:

This is a package that lets you process UMI-4C data from scratch to produce nice plots.

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
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.

python-gseapy 1.0.4
Dependencies: python-wrapper@3.11.11
Propagated dependencies: python-numpy@1.26.4 python-scipy@1.12.0 python-pandas@2.2.3 python-matplotlib@3.8.2 python-requests@2.32.5
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/zqfang/gseapy
Licenses: Modified BSD
Synopsis: Gene Set Enrichment Analysis in Python
Description:

GSEApy is a Python/Rust implementation for GSEA and wrapper for Enrichr. GSEApy can be used for RNA-seq, ChIP-seq, Microarray data. It can be used for convenient GO enrichment and to produce publication quality figures in Python.

plink 1.07
Dependencies: zlib@1.3.1 openblas@0.3.30
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://pngu.mgh.harvard.edu/~purcell/plink/
Licenses: GPL 2 LGPL 2.1+
Synopsis: Whole genome association analysis toolset
Description:

PLINK is a whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.

genrich 0.5
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/jsh58/Genrich
Licenses: Expat
Synopsis: Detecting sites of genomic enrichment
Description:

Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). It analyzes alignment files generated following the assay and produces a file detailing peaks of significant enrichment.

circtools 1.0.0
Dependencies: bioparser@3.0.13 biosoup@0.10.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/Kevinzjy/circtools
Licenses: Expat
Synopsis: Accelerating functions in CIRI toolkit
Description:

This package provides accelerated functions for the CIRI toolkit. It also provides the ccs executable to scan for circular consensus sequences.

libmaus2 2.0.786
Propagated dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://gitlab.com/german.tischler/libmaus2
Licenses: GPL 2+ GPL 3+
Synopsis: Collection of data structures and algorithms useful for bioinformatics
Description:

libmaus2 is a collection of data structures and algorithms. It contains:

  • I/O classes (single byte and UTF-8);

  • bitio classes (input, output and various forms of bit level manipulation);

  • text indexing classes (suffix and LCP array, fulltext and minute (FM), etc.);

  • BAM sequence alignment files input/output (simple and collating); and many lower level support classes.

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+
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.

sailfish 0.10.1
Dependencies: boost@1.83.0 eigen@3.4.0 jemalloc@5.3.0 jellyfish@2.3.0 sparsehash@2.0.4 libdivsufsort@2.0.1 libgff@2.0.0 tbb@2020.3 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.cs.cmu.edu/~ckingsf/software/sailfish/
Licenses: GPL 3+
Synopsis: Mapping-based isoform quantification from RNA-Seq reads
Description:

Sailfish is a tool for genomic transcript quantification from RNA-seq data. It requires a set of target transcripts (either from a reference or de-novo assembly) to quantify. All you need to run sailfish is a fasta file containing your reference transcripts and a (set of) fasta/fastq file(s) containing your reads.

tadbit 1.0.1-2.2838129
Dependencies: imp@2.23.0 mcl@14.137 python-future@1.0.0 python-h5py@3.13.0 python-scipy@1.12.0 python-numpy@1.26.4 python-matplotlib@3.8.2 python-pysam@0.23.0 r-minimal@4.5.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://3dgenomes.github.io/TADbit/
Licenses: GPL 3+
Synopsis: Analyze, model, and explore 3C-based data
Description:

TADbit is a complete Python library to deal with all steps to analyze, model, and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models.

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