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

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.


python-doubletdetection 4.2
Propagated dependencies: python-anndata@0.12.1 python-ipywidgets@8.1.2 python-leidenalg@0.10.2 python-louvain-igraph@0.8.2 python-matplotlib@3.8.2 python-numpy@1.26.4 python-pandas@2.2.3 python-phenograph@1.5.7 python-scanpy@1.11.2 python-scipy@1.12.0 python-tqdm@4.67.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/JonathanShor/DoubletDetection
Licenses: Expat
Build system: pyproject
Synopsis: This is a package to detect doublets in single-cell RNA-seq count matrices
Description:

This package provides a method to detect and enable removal of doublets from single-cell RNA-sequencing.

homer 4.11.1
Dependencies: perl@5.36.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://homer.ucsd.edu/homer
Licenses: GPL 3+
Build system: gnu
Synopsis: Motif discovery and next generation sequencing analysis
Description:

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. It is a collection of command line programs written in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding 8-20 bp motifs in large scale genomics data. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.

r-saige 1.3.4-2.44c8dd4
Dependencies: openblas@0.3.30 plink-ng@2.0.0-a.6.16 savvy@2.1.0 superlu@5.3.0 zlib@1.3.1 zstd@1.5.6
Propagated dependencies: r-bh@1.87.0-1 r-data-table@1.17.8 r-dplyr@1.1.4 r-lintools@0.1.7 r-matrix@1.7-4 r-metaskat@0.90 r-optparse@1.7.5 r-qlcmatrix@0.9.9 r-rcpp@1.1.0 r-rcpparmadillo@15.2.2-1 r-rcppeigen@0.3.4.0.2 r-rcppparallel@5.1.11-1 r-rhpcblasctl@0.23-42 r-rsqlite@2.4.4 r-skat@2.2.5 r-spatest@3.1.2 r-survival@3.8-3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/saigegit/SAIGE
Licenses: GPL 2+
Build system: r
Synopsis: Genome-wide association tests in large-scale data sets
Description:

SAIGE is a package for efficiently controlling for case-control imbalance and sample relatedness in single-variant assoc tests (SAIGE) and controlling for sample relatedness in region-based assoc tests in large cohorts and biobanks (SAIGE-GENE+).

smithlab-cpp 0.1.728a097
Dependencies: samtools@0.1.19 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/smithlabcode/smithlab_cpp
Licenses: GPL 3+
Build system: gnu
Synopsis: C++ helper library for functions used in Smith lab projects
Description:

Smithlab CPP is a C++ library that includes functions used in many of the Smith lab bioinformatics projects, such as a wrapper around Samtools data structures, classes for genomic regions, mapped sequencing reads, etc.

flash 1.2.11
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://ccb.jhu.edu/software/FLASH/
Licenses: GPL 3+
Build system: gnu
Synopsis: Merge paired-end nucleotide reads from NGS experiments
Description:

FLASH (Fast Length Adjustment of SHort reads) is a tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data.

eddylab-squid 1.9g
Dependencies: perl@5.36.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://eddylab.org/software.html
Licenses: GPL 2
Build system: gnu
Synopsis: C function library for sequence analysis
Description:

SQUID is Sean Eddy's personal library of C functions and utility programs for sequence analysis.

python-mofapy2 0.7.1
Propagated dependencies: python-anndata@0.12.1 python-h5py@3.13.0 python-numpy@1.26.4 python-pandas@2.2.3 python-scikit-learn@1.7.0 python-scipy@1.12.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://biofam.github.io/MOFA2/
Licenses: LGPL 3
Build system: pyproject
Synopsis: Multi-omics factor analysis
Description:

MOFA is a factor analysis model that provides a general framework for the integration of multi-omic data sets in an unsupervised fashion. Intuitively, MOFA can be viewed as a versatile and statistically rigorous generalization of principal component analysis to multi-omics data. Given several data matrices with measurements of multiple -omics data types on the same or on overlapping sets of samples, MOFA infers an interpretable low-dimensional representation in terms of a few latent factors. These learnt factors represent the driving sources of variation across data modalities, thus facilitating the identification of cellular states or disease subgroups.

piranha 1.2.1-1.0466d36
Dependencies: bamtools@2.5.2 samtools@0.1.19 gsl@2.8
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/smithlabcode/piranha
Licenses: GPL 3+
Build system: gnu
Synopsis: Peak-caller for CLIP-seq and RIP-seq data
Description:

Piranha is a peak-caller for genomic data produced by CLIP-seq and RIP-seq experiments. It takes input in BED or BAM format and identifies regions of statistically significant read enrichment. Additional covariates may optionally be provided to further inform the peak-calling process.

r-tsis 0.2.0-1.2446029
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/wyguo/TSIS
Licenses: GPL 3
Build system: r
Synopsis: Time-series isoform switch of alternative splicing
Description:

TSIS is used for detecting transcript isoform switches in time-series data. Transcript isoform switches occur when a pair of alternatively spliced isoforms reverse the order of their relative expression levels. TSIS characterizes the transcript switch by defining the isoform switch time-points for any pair of transcript isoforms within a gene. In addition, this tool describes the switch using five different features or metrics. Also it filters the results with user’s specifications and visualizes the results using different plots for the user to examine further details of the switches.

r-ewastools 1.7.2-1.f7646ca
Propagated dependencies: r-data-table@1.17.8 r-igraph@2.2.1 r-illuminaio@0.52.0 r-mblm@0.12.1 r-quadprog@1.5-8
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/hhhh5/ewastools/
Licenses: Unlicense
Build system: r
Synopsis: Quality control toolset for the Illumina Infinium DNA methylation
Description:

This package provides a collection of useful functions for working with DNA methylation micro-array data.

kraken2 2.1.2
Dependencies: gzip@1.14 perl@5.36.0 rsync@3.4.1 sed@4.9 wget@1.25.0 which@2.21
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/DerrickWood/kraken2
Licenses: Expat
Build system: gnu
Synopsis: Taxonomic sequence classification system
Description:

Kraken is a taxonomic sequence classifier that assigns taxonomic labels to DNA sequences. Kraken examines the k-mers within a query sequence and uses the information within those k-mers to query a database. That database maps k-mers to the lowest common ancestor (LCA) of all genomes known to contain a given k-mer.

python-telomerecat 4.0.2
Propagated dependencies: python-click@8.1.8 python-numpy@1.26.4 python-pandas@2.2.3 python-parabam@3.0.1-0.be5bd35 python-pysam@0.23.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/cancerit/telomerecat
Licenses: GPL 3
Build system: pyproject
Synopsis: Telomere computational analysis tool
Description:

Telomerecat is a tool for estimating the average telomere length (TL) for a paired end, whole genome sequencing (WGS) sample.

Telomerecat is adaptable, accurate and fast. The algorithm accounts for sequencing amplification artifacts, anneouploidy (common in cancer samples) and noise generated by WGS. For a high coverage WGS BAM file of around 100GB telomerecat can produce an estimate in ~1 hour.

adapterremoval 2.3.3
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://adapterremoval.readthedocs.io/
Licenses: GPL 3+
Build system: gnu
Synopsis: Rapid sequence adapter trimming, identification, and read merging
Description:

This program searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, the AdapterRemoval may be used to recover a consensus adapter sequence for paired-ended data, for which this information is not available.

stpipeline 2.0.0
Propagated dependencies: htseq@2.0.2 python-distance@0.1.3-0.ad7f9dc python-dnaio@0.10.0 python-numpy@1.26.4 python-pandas@2.2.3 python-pysam@0.23.0 python-regex@2024.11.6 python-scikit-learn@1.7.0 python-scipy@1.12.0 python-seaborn@0.13.2 python-taggd@0.4.0 python-types-regex@2025.9.18.20250921 samtools@1.19 star@2.7.8a
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/jfnavarro/st_pipeline
Licenses: Expat
Build system: pyproject
Synopsis: Pipeline for spatial mapping of unique transcripts
Description:

This package provides an automated pipeline for spatial mapping of unique transcripts.

kaiju 1.9.0
Dependencies: bzip2@1.0.8 coreutils@9.1 curl@8.6.0 gawk@5.3.0 guile@3.0.9 gzip@1.14 perl@5.36.0 python-wrapper@3.11.14 tar@1.35 wget@1.25.0 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://kaiju.binf.ku.dk/
Licenses: GPL 3+
Build system: gnu
Synopsis: Fast and sensitive taxonomic classification for metagenomics
Description:

Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing experiments.

r-phantompeakqualtools 1.2.2-1.8d2b2d1
Dependencies: r-minimal@4.5.2
Propagated dependencies: r-catools@1.18.3 r-snow@0.4-4 r-snowfall@1.84-6.3 r-bitops@1.0-9 r-rsamtools@2.26.0 r-spp@1.16.0 gawk@5.3.0 samtools@1.19 boost@1.89.0 gzip@1.14
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/kundajelab/phantompeakqualtools
Licenses: Modified BSD
Build system: gnu
Synopsis: Informative enrichment for ChIP-seq data
Description:

This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.

python-parabam 3.0.1-0.be5bd35
Propagated dependencies: python-numpy@1.26.4 python-pysam@0.23.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/cancerit/parabam
Licenses: GPL 3
Build system: pyproject
Synopsis: Parallel BAM File Analysis
Description:

Parabam is a tool for processing sequencing files in parallel. It uses Python's native multiprocessing framework to apply a user defined rule on an input file.

umi-tools 1.1.6
Dependencies: python-pandas@2.2.3 python-future@1.0.0 python-scipy@1.12.0 python-matplotlib@3.8.2 python-regex@2024.11.6 python-pybktree@1.1 python-scipy@1.12.0 python-pysam@0.23.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/CGATOxford/UMI-tools
Licenses: Expat
Build system: pyproject
Synopsis: Tools for analyzing unique modular identifiers
Description:

This package provides tools for dealing with Unique Molecular Identifiers (UMIs) and Random Molecular Tags (RMTs) in genetic sequences. There are six tools: the extract and whitelist commands are used to prepare a fastq containing UMIs +/- cell barcodes for alignment. The remaining commands, group, dedup, and count/count_tab, are used to identify PCR duplicates using the UMIs and perform different levels of analysis depending on the needs of the user.

sambamba 0.8.2
Dependencies: ldc@1.38.0 lz4@1.10.0 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/biod/sambamba
Licenses: GPL 2+
Build system: gnu
Synopsis: Tools for working with SAM/BAM data
Description:

Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current parallelised functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth.

kallisto 0.50.1
Dependencies: hdf5@1.14.6 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://pachterlab.github.io/kallisto/
Licenses: FreeBSD
Build system: cmake
Synopsis: Near-optimal RNA-Seq quantification
Description:

Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. Pseudoalignment of reads preserves the key information needed for quantification, and kallisto is therefore not only fast, but also as accurate as existing quantification tools.

python-ngesh 1.0
Propagated dependencies: python-ete3@3.1.3 python-numpy@1.26.4 python-six@1.17.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/tresoldi/ngesh
Licenses: Expat
Build system: pyproject
Synopsis: Library for phylogenetic tree simulation
Description:

Ngesh is a Python library and CLI tool for simulating phylogenetic trees and data. It is intended for benchmarking phylogenetic methods, especially in historical linguistics andstemmatology. The generation of stochastic phylogenetic trees also goes by the name simulationmethods for phylogenetic trees, synthetic data generation, or just phylogenetic tree simulation.

python-bcbio-gff 0.7.1
Propagated dependencies: python-biopython@1.85 python-six@1.17.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/chapmanb/bcbb/tree/master/gff
Licenses: non-copyleft
Build system: pyproject
Synopsis: Read and write GFF files with Biopython integration
Description:

This package lets you read and write files in Generic Feature Format (GFF) with Biopython integration.

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.

velvet 1.2.10
Dependencies: openmpi@4.1.6 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.ebi.ac.uk/~zerbino/velvet/
Licenses: GPL 2+
Build system: gnu
Synopsis: Nucleic acid sequence assembler for very short reads
Description:

Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454. Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired read information, if available, to retrieve the repeated areas between contigs.

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Total results: 69112