_            _    _        _         _
      /\ \         /\ \ /\ \     /\_\      / /\
      \_\ \       /  \ \\ \ \   / / /     / /  \
      /\__ \     / /\ \ \\ \ \_/ / /     / / /\ \__
     / /_ \ \   / / /\ \ \\ \___/ /     / / /\ \___\
    / / /\ \ \ / / /  \ \_\\ \ \_/      \ \ \ \/___/
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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.


sharc 1.0-sge
Dependencies: gawk@5.3.0 bash@5.2.37 coreutils@9.1 emboss@6.5.7 grep@3.11 grid-engine-core@8.1.9 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.

assembly-stats 1.0.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/sanger-pathogens
Licenses: GPL 3
Build system: cmake
Synopsis: Tool to extract assembly statistics from FASTA and FASTQ files
Description:

This package provides a tool to extract assembly statistics from FASTA and FASTQ files.

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.

metamaps 0.0-1.e23f8a8
Dependencies: boost@1.89.0 gsl@2.8 zlib@1.3.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/DiltheyLab/MetaMaps
Licenses: Public Domain
Build system: gnu
Synopsis: Long-read metagenomic analysis
Description:

MetaMaps is tool specifically developed for the analysis of long-read (PacBio/Oxford Nanopore) metagenomic datasets.

r-nichenetr 2.0.4
Propagated dependencies: r-caret@7.0-1 r-catools@1.18.3 r-circlize@0.4.16 r-complexheatmap@2.26.0 r-cowplot@1.2.0 r-data-table@1.17.8 r-diagrammer@1.0.11 r-dicekriging@1.6.1 r-dplyr@1.1.4 r-e1071@1.7-16 r-emoa@0.5-3 r-fdrtool@1.2.18 r-ggforce@0.5.0 r-ggnewscale@0.5.2 r-ggplot2@4.0.1 r-ggpubr@0.6.2 r-hmisc@5.2-4 r-igraph@2.2.1 r-limma@3.66.0 r-magrittr@2.0.4 r-matrix@1.7-4 r-mlrmbo@1.1.5.1 r-parallelmap@1.5.1 r-purrr@1.2.0 r-randomforest@4.7-1.2 r-readr@2.1.6 r-rocr@1.0-11 r-seurat@5.3.1 r-shadowtext@0.1.6 r-tibble@3.3.0 r-tidyr@1.3.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/saeyslab/nichenetr
Licenses: GPL 3
Build system: r
Synopsis: R implementation of the NicheNet method
Description:

The goal of NicheNet is to study intercellular communication from a computational perspective. NicheNet uses human or mouse gene expression data of interacting cells as input and combines this with a prior model that integrates existing knowledge on ligand-to-target signaling paths. This allows to predict ligand-receptor interactions that might drive gene expression changes in cells of interest.

python-formulaic-contrasts 1.0.0
Propagated dependencies: python-formulaic@1.0.1 python-pandas@2.2.3 python-session-info@1.0.0
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/scverse/formulaic-contrasts
Licenses: Modified BSD
Build system: pyproject
Synopsis: Build contrasts for models defined with formulaic
Description:

Build contrasts for models defined with formulaic.

perl-bio-pipeline-comparison 1.123050
Dependencies: bioperl-minimal@1.7.0 perl-exception-class@1.44 perl-file-which@1.23 perl-moose@2.2015 perl-try-tiny@0.31
Propagated dependencies: htslib@1.21 which@2.21
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://search.cpan.org/dist/Bio-Pipeline-Comparison
Licenses: GPL 3+
Build system: perl
Synopsis: Comparative assesment of variant calling (CAVar)
Description:
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.

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.

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:
last 1080
Dependencies: zlib@1.3.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://last.cbrc.jp/
Licenses: GPL 3
Build system: gnu
Synopsis: Genome-scale sequence comparison
Description:
perl-acme-damn 0.08
Dependencies: perl-test-exception@0.43
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://search.cpan.org/dist/Acme-Damn
Licenses: GPL 1+
Build system: perl
Synopsis: 'Unbless' Perl objects.
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.

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.

perl-set-intervaltree 0.10
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://search.cpan.org/dist/Set-IntervalTree
Licenses: GPL 1+
Build system: perl
Synopsis: Perform range-based lookups on sets of ranges.
Description:
perl-parallel-iterator 1.00
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://search.cpan.org/dist/Parallel-Iterator
Licenses: GPL 1+
Build system: perl
Synopsis: Simple parallel execution
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-nanofilt 2.8.0
Propagated dependencies: python-biopython@1.85 python-pandas@2.2.3
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/wdecoster/nanofilt
Licenses: GPL 3
Build system: pyproject
Synopsis: Filtering and trimming of Oxford Nanopore Sequencing data
Description:

This package provides tools for filtering on quality and/or read length, and optional trimming after passing filters. Reads from stdin, writes to stdout. Optionally reads directly from an uncompressed file specified on the command line. It is intended to be used directly after fastq extraction, prior to mapping, or in a stream between extraction and mapping.

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.

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

strelka 2.9.2
Dependencies: boost@1.89.0 perl@5.36.0 bash@5.2.37 zlib@1.3.1 samtools@1.19 rapidjson@1.1.0-1.949c771 codemin@1.0.5 curl@8.6.0 xz@5.4.5 openssl@3.0.8 samtools@0.1.19 zlib@1.3.1 python@3.11.14
Propagated dependencies: vcftools@0.1.16 htslib@1.21
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/Illumina/strelka
Licenses: GPL 3+
Build system: cmake
Synopsis: Small variant caller
Description:

Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs. The germline caller employs an efficient tiered haplotype model to improve accuracy and provide read-backed phasing, adaptively selecting between assembly and a faster alignment-based haplotyping approach at each variant locus. The germline caller also analyzes input sequencing data using a mixture-model indel error estimation method to improve robustness to indel noise. The somatic calling model improves on the original Strelka method for liquid and late-stage tumor analysis by accounting for possible tumor cell contamination in the normal sample. A final empirical variant re-scoring step using random forest models trained on various call quality features has been added to both callers to further improve precision.

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Total results: 68655