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

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.


igv 2.16.2
Propagated dependencies: openjdk@11.0.22
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://www.broadinstitute.org/software/igv/
Licenses: Expat
Build system: gnu
Synopsis: Integrative Genomics Viewer
Description:

The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

freec 11.6b
Dependencies: perl@5.36.0
Propagated dependencies: r-rtracklayer@1.70.0
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://bioinfo-out.curie.fr/projects/freec/
Licenses: GPL 2+
Build system: gnu
Synopsis: Tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data
Description:

Control-FREEC automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. The control (matched normal) sample is optional for whole genome sequencing data but mandatory for whole exome or targeted sequencing data. For whole genome sequencing data analysis, the program can also use mappability data (files created by GEM).

cat 5.2.3
Dependencies: diamond@2.1.6 prodigal@2.6.3 python@3.11.14
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/dutilh/CAT
Licenses: Expat
Build system: gnu
Synopsis: Tool for taxonomic classification of contigs and metagenome-assembled genomes
Description:

Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. CAT and BAT can be run from intermediate steps if files are formated appropriately

perl-forks 0.36
Propagated dependencies: perl-acme-damn@0.08 perl-devel-symdump@2.18 perl-list-moreutils@0.430 perl-sys-sigaction@0.23
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://search.cpan.org/dist/forks
Licenses: GPL 1+
Build system: perl
Synopsis: forks - emulate threads with fork
Description:
libmaus 0.0.196
Dependencies: zlib@1.3.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/gt1/libmaus
Licenses: GPL 3+
Build system: gnu
Synopsis: Collection of bioinformatics data structures and algorithms
Description:

This package contains a collection of bioinformatics data structures and algorithms. It provides I/O classes, bitio classes, text indexing classes and BAM sequence alignment functionality.

python-primer3-py 2.2.0
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://libnano.github.io/primer3-py/
Licenses: GPL 2
Build system: pyproject
Synopsis: Simple oligo analysis and primer design
Description:

Primer3-py is a Python-abstracted API for the popular Primer3 library. The intention is to provide a simple and reliable interface for automated oligo analysis and design.

Primer3-py also includes bindings for the Primer3 primer design engine if you’d prefer to use an established pipeline. The IO parameters mirror those of the original Primer3, but you don’t have to deal with messy and slow file IO for your automated workflows.

bioparser 3.1.0
Dependencies: biosoup@0.11.0
Propagated dependencies: zlib@1.3.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/rvaser/bioparser
Licenses: Expat
Build system: cmake
Synopsis: C++ library for parsing several formats in bioinformatics
Description:

Bioparser is a C++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.

perl-prokka 1.14.6
Dependencies: aragorn@1.2.41 bioperl-minimal@1.7.0 blast+@2.17.0 findutils@4.10.0 hmmer@3.3.2 infernal@1.1.4 minced@0.3.2 parallel@20251122 perl@5.36.0 perl-data-dumper@2.183 perl-digest-md5@2.58 perl-findbin-libs@2.15 perl-module-build@0.4231 perl-scalar-list-utils@1.62 perl-time-piece@1.3401 perl-xml-simple@2.25 prodigal@2.6.3
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/tseemann/prokka
Licenses: GPL 3
Build system: gnu
Synopsis: Rapid prokaryotic genome annotation
Description:

This package provides tools for rapid prokaryotic genome annotation.

perl-sys-sigaction 0.23
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://search.cpan.org/dist/Sys-SigAction
Licenses: GPL 1+
Build system: perl
Synopsis: Perl extension for Consistent Signal Handling
Description:
sharc 1.0-slurm
Dependencies: gawk@5.3.0 bash@5.2.37 coreutils@9.1 emboss@6.5.7 grep@3.11 qsub-slurm@0.0.7 minimap2@2.28 primer3@2.6.1 perl@5.36.0 python@3.11.14 python-aniso8601@10.0.1 python-certifi@2025.06.15 python-chardet@5.2.0 python-configparser@7.2.0 python-flask@3.1.0 python-flask-restful@0.3.10 python-idna@3.10 python-itsdangerous@2.2.0 python-jinja2@3.1.2 python-markupsafe@3.0.2 nanosv@1.2.4 python-pymongo@4.14.0 python-pysam@0.23.0 python-pytz@2025.1 python-pyvcf3@1.0.3-0.1fb3789 python-requests@2.32.5 python-six@1.17.0 python-urllib3@2.5.0 python-werkzeug@3.1.3 python2@2.7.18 r-minimal@4.5.2 r-ggplot2@4.0.1 r-randomforest@4.7-1.2 r-rocr@1.0-11 sambamba@0.8.2 sed@4.9 gnomad-sv-sites@2.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/UMCUGenetics/SHARC
Licenses: GPL 3
Build system: gnu
Synopsis: Somatic SV pipeline for tumor-only Nanopore sequencing data
Description:

SHARC is a pipeline for somatic SV calling and filtering from tumor-only Nanopore sequencing data. It performs mapping, SV calling, SV filtering, random forest classification, blacklist filtering and SV prioritization, followed by automated primer design for PCR amplicons of 80-120 bp that are useful to track cancer ctDNA molecules in liquid biopsies.

primer3 2.6.1
Dependencies: perl@5.36.0
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://primer3.org/
Licenses: GPL 2
Build system: gnu
Synopsis: Tool to select primers for polymerase chain reaction
Description:

Primer3 is a widely used program for designing PCR primers. PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.

perl-term-ui 0.50
Propagated dependencies: perl-log-message-simple@0.10
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://search.cpan.org/dist/Term-UI
Licenses: GPL 1+
Build system: perl
Synopsis: User interfaces via Term::ReadLine made easy
Description:
perl-findbin-libs 2.15
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://search.cpan.org/dist/FindBin-libs
Licenses: GPL 1+
Build system: perl
Synopsis:
Description:
biosoup 0.11.0
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/rvaser/biosoup
Licenses: Expat
Build system: cmake
Synopsis: C++ support library for bioinformatics tools
Description:

Biosoup is a C++ collection of header-only data structures used for storage and logging in bioinformatics tools.

hiddendomains 3.1
Dependencies: perl@5.36.0
Propagated dependencies: r-depmixs4@1.5-1 r-hiddenmarkov@1.8-14
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://hiddendomains.sourceforge.net
Licenses: GPL 2
Build system: gnu
Synopsis: Programs used to identify enrichment of ChIP-seq reads
Description:

hiddenDomains is a suite of programs used to identify significant enrichment of ChIP-seq reads that span large domains, like HK27me3. The input data can be in BAM format, or in a tab-delimited 'reads per bin' format described below. The output is a BED formatted file the lists the enriched domains and their posterior probabilities.

easel 0.49
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://bioeasel.org/
Licenses: FreeBSD
Build system: gnu
Synopsis: Sequence analysis library from The Eddy/Rivas Laboratory
Description:

Easel is an ANSI C code library developed by the Eddy/Rivas laboratory at Harvard. Easel supports our work on computational analysis of biological sequences using probabilistic models. Easel is used by HMMER, the profile hidden Markov model software that underlies several protein and DNA sequence family databases such as Pfam, and by Infernal, the profile stochastic context-free grammar software that underlies the Rfam RNA family database. Easel aims to make similar applications more robust and easier to develop, by providing a set of reusable, documented, and well-tested functions.

star 2.4.2a
Dependencies: htslib@1.21 zlib@1.3.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science 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.

python-anvio 8
Propagated dependencies: python-bottle@0.13.4 python-colored@2.3.0 python-django@5.2.8 python-ete3@3.1.3 python-illumina-utils@2.13 python-matplotlib@3.8.2 python-mistune@3.1.3 python-multiprocess@0.70.18 python-networkx@3.4.2 python-numba@0.61.0 python-numpy@1.26.4 python-pandas@2.2.3 python-paste@3.10.1 python-plotext@5.2.8 python-psutil@7.0.0 python-pyani@0.2.12 python-pysam@0.23.0 python-requests@2.32.5 python-rich-argparse@1.7.1 python-scikit-learn@1.7.0 python-scipy@1.12.0 python-six@1.17.0 python-statsmodels@0.14.4 python-tabulate@0.9.0 snakemake@8.29.2
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://anvio.org
Licenses: GPL 3+
Build system: pyproject
Synopsis: Analysis and visualization platform for 'omics data
Description:

Anvi’o is a comprehensive platform that brings together many aspects of today’s computational strategies of data-enabled microbiology, including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in an integrated and easy-to-use fashion through extensive interactive visualization capabilities.

sharc 1.0-local
Dependencies: gawk@5.3.0 bash@5.2.37 coreutils@9.1 emboss@6.5.7 grep@3.11 qsub-local@0.0.1 minimap2@2.28 primer3@2.6.1 perl@5.36.0 python@3.11.14 python-aniso8601@10.0.1 python-certifi@2025.06.15 python-chardet@5.2.0 python-configparser@7.2.0 python-flask@3.1.0 python-flask-restful@0.3.10 python-idna@3.10 python-itsdangerous@2.2.0 python-jinja2@3.1.2 python-markupsafe@3.0.2 nanosv@1.2.4 python-pymongo@4.14.0 python-pysam@0.23.0 python-pytz@2025.1 python-pyvcf3@1.0.3-0.1fb3789 python-requests@2.32.5 python-six@1.17.0 python-urllib3@2.5.0 python-werkzeug@3.1.3 python2@2.7.18 r-minimal@4.5.2 r-ggplot2@4.0.1 r-randomforest@4.7-1.2 r-rocr@1.0-11 sambamba@0.8.2 sed@4.9 gnomad-sv-sites@2.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/UMCUGenetics/SHARC
Licenses: GPL 3
Build system: gnu
Synopsis: Somatic SV pipeline for tumor-only Nanopore sequencing data
Description:

SHARC is a pipeline for somatic SV calling and filtering from tumor-only Nanopore sequencing data. It performs mapping, SV calling, SV filtering, random forest classification, blacklist filtering and SV prioritization, followed by automated primer design for PCR amplicons of 80-120 bp that are useful to track cancer ctDNA molecules in liquid biopsies.

spades 4.2.0
Dependencies: bzip2@1.0.8 perl@5.36.0 python@3.11.14 zlib@1.3.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://ablab.github.io/spades/
Licenses: GPL 2
Build system: cmake
Synopsis: Genome assembly toolkit
Description:

SPAdes is an assembly toolkit containing various assembly pipelines.

python-nanoget 1.19.4
Propagated dependencies: python-biopython@1.85 python-numpy@1.26.4 python-pandas@2.2.3 python-pysam@0.23.0
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/wdecoster/nanoget
Licenses: GPL 3
Build system: pyproject
Synopsis: Functions for Oxford Nanopore sequencing data and alignments
Description:

This package contains functions to extract information from Oxford Nanopore sequencing data and alignments.

fastqc 0.11.9
Propagated dependencies: perl@5.36.0 icedtea@2.6.13
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Licenses: GPL 3+ ASL 2.0
Build system: gnu
Synopsis: A quality control tool for high throughput sequence data
Description:

FastQC aims to provide a QC report which can spot problems which originate either in the sequencer or in the starting library material. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.

seqan 3.0.2
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://www.seqan.de
Licenses: Modified BSD
Build system: cmake
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.

score-client 5.0.0
Dependencies: openjdk@11.0.22
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://docs.icgc.org/software/download/#score-client
Licenses: GPL 3
Build system: gnu
Synopsis: Tool to view ICGC data
Description:

This package provides a tool to download or view data in the cloud environments of ICGC.

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Total results: 68658