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

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.


r-scriabin 0.0.0.9000-1.313d15e
Propagated dependencies: r-ade4@1.7-23 r-cellid@1.16.0 r-circlize@0.4.16 r-clipr@0.8.0 r-complexheatmap@2.24.0 r-complexheatmap@2.24.0 r-cowplot@1.1.3 r-dplyr@1.1.4 r-factoextra@1.0.7 r-fsa@0.10.0 r-genefilter@1.90.0 r-ggalluvial@0.12.5 r-ggfittext@0.10.2 r-ggplot2@3.5.2 r-ggsci@3.2.0 r-limma@3.64.1 r-magrittr@2.0.3 r-matrix@1.7-3 r-matrixstats@1.5.0 r-networkd3@0.4.1 r-nichenetr@2.0.4 r-pbapply@1.7-2 r-qlcmatrix@0.9.8 r-scales@1.4.0 r-scater@1.36.0 r-seurat@5.3.0 r-tibble@3.2.1 r-tidyft@0.9.20 r-wgcna@1.73
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/BlishLab/scriabin
Licenses: Expat
Synopsis: Single-cell resolved interaction analysis through binning
Description:

Scriabin aims to provide a comprehensive view of cell-cell communication (CCC). It achieves this without requiring subsampling or aggregation.

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+
Synopsis: Comparative assesment of variant calling (CAVar)
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@1.1.4 perl@5.36.0 python@3.11.11 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@4.5.0 r-ggplot2@3.5.2 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
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.

perl-cgpvcf 2.0.4
Propagated dependencies: perl-bio-pipeline-comparison@1.123050 perl-const-fast@0.014 perl-data-uuid@1.226 perl-datetime@1.54
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://cancerit.github.io/cgpVcf/
Licenses: AGPL 3+
Synopsis: Set of common Perl utilities for generating VCF headers
Description:

This package contains a set of common Perl utilities for generating consistent Vcf headers. It primarily exists to prevent code duplication between some other projects.

caveman 1.15.5
Dependencies: curl@8.6.0 htslib@1.21 linasm@1.13 perl@5.36.0 zlib@1.3.1
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: http://cancerit.github.io/CaVEMan/
Licenses: AGPL 3+
Synopsis: Implementation of an SNV expectation maximisation algorithm for calling single base substitutions in paired data
Description:

This package provides an implementation of the CaVEMan program. It uses an expectation maximisation approach to calling single base substitutions in paired data. It is designed for use with a compute cluster. Most steps in the program make use of an index parameter. The split step is designed to divide the genome into chunks of adjustable size to optimise for runtime/memory usage requirements.

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+
Synopsis: forks - emulate threads with fork
Description:
allelecount 4.2.1
Dependencies: zlib@1.3.1 htslib@1.21 perl-pod-coverage@0.23 perl-file-which@1.23 perl-test-fatal@0.016 perl-try-tiny@0.31 samtools@1.19
Propagated dependencies: perl-const-fast@0.014 perl-sub-exporter-progressive@0.001013 perl-bio-db-hts@3.01 bioperl-minimal@1.7.0
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/cancerit/alleleCount
Licenses: AGPL 3+
Synopsis: Support code for NGS copy number algorithms
Description:

This package primarily exists to prevent code duplication between some other projects, specifically AscatNGS and Battenburg.

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+
Synopsis: User interfaces via Term::ReadLine made easy
Description:
python-anvio 8
Propagated dependencies: python-bottle@0.13.4 python-colored@2.3.0 python-django@5.2.7 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+
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.

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+
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.

codemin 1.0.5
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/Illumina/strelka/tree/master/redist
Licenses: Expat
Synopsis: Set of lightweight minimization functions.
Description:

The CodeMin minimization library provides a set of lightweight minimization functions originally developed for the CodeAxe phylogenetic analysis package.

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+
Synopsis: Perform range-based lookups on sets of ranges.
Description:
pcap-core 3.5.0
Propagated dependencies: bwa@0.7.18 samtools@1.19 biobambam@0.0.191
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/ICGC-TCGA-PanCancer/PCAP-core
Licenses: GPL 2+
Synopsis: NGS reference implementations and helper code for the ICGC/TCGA Pan-Cancer Analysis Project
Description:
python-pydeseq2 0.5.2
Propagated dependencies: python-anndata@0.11.4 python-formulaic@1.0.1 python-formulaic-contrasts@1.0.0 python-matplotlib@3.8.2 python-numpy@1.26.4 python-pandas@2.2.3 python-scikit-learn@1.7.0 python-scipy@1.12.0
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/owkin/PyDESeq2
Licenses: Expat
Synopsis: Python implementation of DESeq2
Description:

This package provides a python implementation of DESeq2.

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
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.

gnomad-sv-sites 2.1
Dependencies: gzip@1.14
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://gnomad.broadinstitute.org
Licenses: CC0
Synopsis: gnomAD structural variant sites
Description:

This package provides in uncompressed version of the gnomAD structural variant sites.

freec 11.6b
Dependencies: perl@5.36.0
Propagated dependencies: r-rtracklayer@1.68.0
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+
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).

metamaps 0.0-1.e23f8a8
Dependencies: boost@1.83.0 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
Synopsis: Long-read metagenomic analysis
Description:

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

strelka 2.9.2
Dependencies: boost@1.83.0 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@3.11.11
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+
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.

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+
Synopsis: Simple parallel execution
Description:
primer3 1.1.4
Dependencies: perl@5.36.0
Channel: guix-science
Location: guix-science/packages/bioinformatics.scm (guix-science packages bioinformatics)
Home page: https://github.com/primer3-org/primer3
Licenses: GPL 2
Synopsis: Tool to design PCR primers
Description:

Design PCR primers from DNA sequence. From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it.

Page: 12345678910111213141516171819202122232425262728293031323334353637383940414243444546474849505152535455565758596061626364656667686970717273747576777879808182838485868788899091929394959697989910010110210310410510610710810911011111211311411511611711811912012112212312412512612712812913013113213313413513613713813914014114214314414514614714814915015115215315415515615715815916016116216316416516616716816917017117217317417517617717817918018118218318418518618718818919019119219319419519619719819920020120220320420520620720820921021121221321421521621721821922022122222322422522622722822923023123223323423523623723823924024124224324424524624724824925025125225325425525625725825926026126226326426526626726826927027127227327427527627727827928028128228328428528628728828929029129229329429529629729829930030130230330430530630730830931031131231331431531631731831932032132232332432532632732832933033133233333433533633733833934034134234334434534634734834935035135235335435535635735835936036136236336436536636736836937037137237337437537637737837938038138238338438538638738838939039139239339439539639739839940040140240340440540640740840941041141241341441541641741841942042142242342442542642742842943043143243343443543643743843944044144244344444544644744844945045145245345445545645745845946046146246346446546646746846947047147247347447547647747847948048148248348448548648748848949049149249349449549649749849950050150250350450550650750850951051151251351451551651751851952052152252352452552652752852953053153253353453553653753853954054154254354454554654754854955055155255355455555655755855956056156256356456556656756856957057157257357457557657757857958058158258358458558658758858959059159259359459559659759859960060160260360460560660760860961061161261361461561661761861962062162262362462562662762862963063163263363463563663763863964064164264364464564664764864965065165265365465565665765865966066166266366466566666766866967067167267367467567667767867968068168268368468568668768868969069169269369469569669769869970070170270370470570670770870971071171271371471571671771871972072172272372472572672772872973073173273373473573673773873974074174274374474574674774874975075175275375475575675775875976076176276376476576676776876977077177277377477577677777877978078178278378478578678778878979079179279379479579679779879980080180280380480580680780880981081181281381481581681781881982082182282382482582682782882983083183283383483583683783883984084184284384484584684784884985085185285385485585685785885986086186286386486586686786886987087187287387487587687787887988088188288388488588688788888989089189289389489589689789889990090190290390490590690790890991091191291391491591691791891992092192292392492592692792892993093193293393493593693793893994094194294394494594694794894995095195295395495595695795895996096196296396496596696796896997097197297397497597697797897998098198298398498598698798898999099199299399499599699799899910001001100210031004100510061007100810091010101110121013101410151016101710181019102010211022102310241025102610271028102910301031103210331034103510361037103810391040104110421043104410451046104710481049105010511052105310541055105610571058105910601061106210631064106510661067106810691070107110721073107410751076107710781079108010811082108310841085108610871088108910901091109210931094109510961097109810991100110111021103110411051106110711081109111011111112111311141115111611171118111911201121112211231124112511261127112811291130113111321133113411351136113711381139114011411142114311441145114611471148114911501151115211531154115511561157115811591160116111621163116411651166116711681169117011711172117311741175117611771178117911801181118211831184118511861187118811891190119111921193119411951196119711981199120012011202120312041205120612071208120912101211121212131214121512161217121812191220122112221223122412251226122712281229123012311232123312341235123612371238123912401241124212431244124512461247124812491250125112521253125412551256125712581259126012611262126312641265126612671268126912701271127212731274127512761277127812791280128112821283128412851286128712881289129012911292129312941295129612971298129913001301130213031304130513061307130813091310131113121313131413151316131713181319132013211322132313241325132613271328132913301331133213331334133513361337133813391340134113421343134413451346134713481349135013511352135313541355135613571358135913601361136213631364136513661367136813691370137113721373137413751376137713781379138013811382138313841385138613871388138913901391139213931394139513961397139813991400140114021403140414051406140714081409141014111412141314141415141614171418141914201421142214231424142514261427142814291430143114321433143414351436143714381439144014411442144314441445144614471448144914501451145214531454145514561457145814591460146114621463146414651466146714681469147014711472147314741475147614771478147914801481148214831484148514861487148814891490149114921493149414951496149714981499150015011502150315041505150615071508150915101511151215131514151515161517151815191520152115221523152415251526152715281529153015311532153315341535153615371538153915401541154215431544154515461547154815491550155115521553155415551556155715581559156015611562156315641565156615671568156915701571157215731574157515761577157815791580158115821583158415851586158715881589159015911592159315941595159615971598159916001601160216031604160516061607160816091610161116121613161416151616161716181619162016211622162316241625162616271628162916301631163216331634163516361637163816391640164116421643164416451646164716481649165016511652165316541655165616571658165916601661166216631664166516661667166816691670167116721673167416751676167716781679168016811682168316841685168616871688168916901691169216931694169516961697169816991700170117021703170417051706170717081709171017111712171317141715171617171718171917201721172217231724172517261727172817291730173117321733173417351736173717381739174017411742174317441745174617471748174917501751175217531754175517561757175817591760176117621763176417651766176717681769177017711772177317741775177617771778177917801781178217831784178517861787178817891790179117921793179417951796179717981799180018011802180318041805180618071808180918101811181218131814181518161817181818191820182118221823182418251826182718281829183018311832183318341835183618371838183918401841184218431844184518461847184818491850185118521853185418551856185718581859186018611862186318641865186618671868186918701871187218731874187518761877187818791880
Total results: 45109