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


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
Build system: pyproject
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.

snap-aligner 2.0.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://snap.cs.berkeley.edu/
Licenses: ASL 2.0
Build system: gnu
Synopsis: Short read DNA sequence aligner
Description:

SNAP is a fast and accurate aligner for short DNA reads. It is optimized for modern read lengths of 100 bases or higher, and takes advantage of these reads to align data quickly through a hash-based indexing scheme.

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
Build system: ant
Synopsis: Model species geographic distributions
Description:

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

stringtie 3.0.2
Dependencies: bzip2@1.0.8 htslib@1.21 libdeflate@1.19 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://ccb.jhu.edu/software/stringtie/
Licenses: Expat
Build system: gnu
Synopsis: Transcript assembly and quantification for RNA-Seq data
Description:

StringTie is a fast and efficient assembler of RNA-Seq sequence alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments of longer sequences that have been assembled from those reads. To identify differentially expressed genes between experiments, StringTie's output can be processed either by the Cuffdiff or Ballgown programs.

libbigwig 0.4.4
Dependencies: zlib@1.3.1 curl@8.6.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/dpryan79/libBigWig
Licenses: Expat
Build system: gnu
Synopsis: C library for handling bigWig files
Description:

This package provides a C library for parsing local and remote BigWig files.

chromap 0.2.7
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/haowenz/chromap
Licenses: Expat
Build system: gnu
Synopsis: Fast alignment and preprocessing of chromatin profiles
Description:

Chromap is a fast method for aligning and preprocessing high throughput chromatin profiles. Typical use cases include:

  • trimming sequencing adapters, mapping bulk ATAC-seq or ChIP-seq genomic reads to the human genome and removing duplicates;

  • trimming sequencing adapters, mapping single cell ATAC-seq genomic reads to the human genome, correcting barcodes, removing duplicates and performing Tn5 shift;

  • split alignment of Hi-C reads against a reference genome.

r-gutils 0.2.0-2.fc24db6
Propagated dependencies: r-biocgenerics@0.56.0 r-data-table@1.17.8 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-matrix@1.7-4 r-s4vectors@0.48.0 r-stringr@1.6.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/mskilab/gUtils
Licenses: GPL 2
Build system: r
Synopsis: Additional capabilities and speed for GenomicRanges operations
Description:

This is an R package providing additional capabilities and speed for GenomicRanges operations.

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.

bedtools 2.31.1
Dependencies: samtools@1.19 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/arq5x/bedtools2
Licenses: Expat
Build system: gnu
Synopsis: Tools for genome analysis and arithmetic
Description:

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.

seqtk 1.3
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/lh3/seqtk
Licenses: Expat
Build system: gnu
Synopsis: Toolkit for processing biological sequences in FASTA/Q format
Description:

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can be optionally compressed by gzip.

python-cgatcore 0.6.16
Dependencies: time@1.9
Propagated dependencies: python-apsw@3.46.0.0 python-gevent@24.11.1 python-pandas@2.2.3 python-paramiko@4.0.0 python-pyyaml@6.0.2 python-ruffus@2.8.4 python-sqlalchemy@1.4.42
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/cgat-developers/cgat-core
Licenses: Expat
Build system: pyproject
Synopsis: Computational genomics analysis toolkit
Description:

CGAT-core is a set of libraries and helper functions used to enable researchers to design and build computational workflows for the analysis of large-scale data-analysis.

pigx-scrnaseq 1.1.10
Dependencies: coreutils@9.1 perl@5.36.0 fastqc@0.11.9 flexbar@3.4.0 icedtea@3.19.0 jellyfish@2.3.0 python-wrapper@3.11.14 python-pyyaml@6.0.2 python-pandas@2.2.3 python-magic@0.4.27 python-numpy@1.26.4 python-loompy@3.0.7 pandoc@2.19.2 samtools@1.19 snakemake@5.32.2 star@2.7.3a r-minimal@4.5.2 r-argparser@0.7.2 r-cowplot@1.2.0 r-data-table@1.17.8 r-delayedarray@0.36.0 r-delayedmatrixstats@1.32.0 r-dplyr@1.1.4 r-dropbead@0-2.d746c6f r-dt@0.34.0 r-genomicalignments@1.46.0 r-genomicfiles@1.46.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-hdf5array@1.38.0 r-pheatmap@1.0.13 r-rmarkdown@2.30 r-rsamtools@2.26.0 r-rtracklayer@1.70.0 r-rtsne@0.17 r-scater@1.38.0 r-scran@1.38.0 r-seurat@5.3.1 r-singlecellexperiment@1.32.0 r-stringr@1.6.0 r-yaml@2.3.10
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://bioinformatics.mdc-berlin.de/pigx/
Licenses: GPL 3+
Build system: gnu
Synopsis: Analysis pipeline for single-cell RNA sequencing experiments
Description:

PiGX scRNAseq is an analysis pipeline for preprocessing and quality control for single cell RNA sequencing experiments. The inputs are read files from the sequencing experiment, and a configuration file which describes the experiment. It produces processed files for downstream analysis and interactive quality reports. The pipeline is designed to work with UMI based methods.

ngs-bits 2025_09
Dependencies: bzip2@1.0.8 curl@8.6.0 htslib@1.21 libdeflate@1.19 libxml2@2.14.6 lzip@1.25 openssl@3.0.8 qtbase@5.15.17 qtsvg@5.15.17 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/imgag/ngs-bits
Licenses: Expat
Build system: gnu
Synopsis: Short-read and long-read sequencing tools for diagnostics
Description:

Ngs-bits (Next-Generation Sequencing) is collection of short-read and long-read sequencing tools for diagnostics.

vembrane 1.0.7
Dependencies: python-asttokens@3.0.0 python-intervaltree@3.1.0 python-numpy@1.26.4 python-pysam@0.23.0 python-pyyaml@6.0.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/vembrane/vembrane
Licenses: Expat
Build system: pyproject
Synopsis: Filter VCF/BCF files with Python expressions
Description:

Vembrane simultaneously filters variants based on any INFO or FORMAT field, CHROM, POS, ID, REF, ALT, QUAL, FILTER, and the annotation field ANN. When filtering based on ANN, annotation entries are filtered first. If no annotation entry remains, the entire variant is deleted.

emboss 6.5.7
Dependencies: perl@5.36.0 libpng@1.6.39 gd@2.3.3 libx11@1.8.12 libharu@2.4.3 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://emboss.sourceforge.net
Licenses: GPL 2+
Build system: gnu
Synopsis: Molecular biology analysis suite
Description:

EMBOSS is the "European Molecular Biology Open Software Suite". EMBOSS is an analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. It also provides a number of libraries for the development of software in the field of molecular biology. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole.

seek 1-1.196ed4c
Dependencies: apache-thrift@0.14.2 apache-thrift@0.14.2 gsl@2.8 boost@1.89.0 gengetopt@2.23 libsvm@336 log4cpp@1.1.3 python@3.11.14 readline@8.2.13
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://seek.princeton.edu
Licenses: CC-BY 3.0
Build system: cmake
Synopsis: Gene co-expression search engine
Description:

SEEK is a computational gene co-expression search engine. SEEK provides biologists with a way to navigate the massive human expression compendium that now contains thousands of expression datasets. SEEK returns a robust ranking of co-expressed genes in the biological area of interest defined by the user's query genes. It also prioritizes thousands of expression datasets according to the user's query of interest.

fit-sne 1.2.1
Dependencies: fftw@3.3.10
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/KlugerLab/FIt-SNE
Licenses: Original BSD Expat ASL 2.0
Build system: gnu
Synopsis: Fast Fourier Transform-accelerated interpolation-based t-SNE
Description:

t-Stochastic Neighborhood Embedding (t-SNE) is a method for dimensionality reduction and visualization of high dimensional datasets. A popular implementation of t-SNE uses the Barnes-Hut algorithm to approximate the gradient at each iteration of gradient descent. This implementation differs in these ways:

  • Instead of approximating the N-body simulation using Barnes-Hut, we interpolate onto an equispaced grid and use FFT to perform the convolution.

  • Instead of computing nearest neighbors using vantage-point trees, we approximate nearest neighbors using the Annoy library. The neighbor lookups are multithreaded to take advantage of machines with multiple cores.

python-splicekit 0.7
Propagated dependencies: python-beautifulsoup4@4.14.3 python-dateutil@2.9.0 python-levenshtein@0.27.1 python-logomaker@0.8.7 python-numpy@1.26.4 python-pandas@2.2.3 python-plotly@5.20.0 python-psutil@7.0.0 python-pybio@0.3.12-1.c91fddc python-pysam@0.23.0 python-rangehttpserver@1.4.0 python-requests@2.32.5 python-scanrbp@0.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/bedapub/splicekit
Licenses: GPL 3
Build system: pyproject
Synopsis: Python toolkit for splicing analysis from short-read RNA-seq
Description:

Splicekit is a modular platform for splicing analysis from short-read RNA-seq datasets. The platform also integrates pybio for genomic operations and scanRBP for RNA-protein binding studies. The whole analysis is self-contained (one single directory) and the platform is written in Python, in a modular way.

tetoolkit 2.2.3
Dependencies: bash-minimal@5.2.37 coreutils@9.1 bedtools@2.31.1 python-pysam@0.23.0 r-minimal@4.5.2 r-deseq2@1.50.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/mhammell-laboratory/TEtranscripts
Licenses: GPL 3+
Build system: pyproject
Synopsis: Transposable elements in differential enrichment analysis
Description:

This is package for including transposable elements in differential enrichment analysis of sequencing datasets. TEtranscripts and TEcount take RNA-seq (and similar data) and annotates reads to both genes and transposable elements. TEtranscripts then performs differential analysis using DESeq2. Note that TEtranscripts and TEcount rely on specially curated GTF files, which are not included due to their size.

python-dna-features-viewer 3.1.1
Propagated dependencies: python-biopython@1.85 python-matplotlib@3.8.2 python-packaging@25.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer
Licenses: Expat
Build system: pyproject
Synopsis: Plot features from DNA sequences
Description:

DNA Features Viewer is a Python library to visualize DNA features, e.g. from GenBank or Gff files, or Biopython SeqRecords.

python-cnmf 1.6.0
Propagated dependencies: python-anndata@0.12.1 python-fastcluster@1.2.6 python-matplotlib@3.8.2 python-numba@0.61.0 python-numpy@1.26.4 python-palettable@3.3.3 python-pandas@2.2.3 python-pyyaml@6.0.2 python-scanpy@1.11.2 python-scikit-learn@1.7.0 python-scipy@1.12.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/dylkot/cNMF
Licenses: Expat
Build system: pyproject
Synopsis: Consensus NMF for scRNA-Seq data
Description:

This tool offers a pipeline for inferring gene expression programs from scRNA-Seq. It takes a count matrix (N cells X G genes) as input and produces a (K x G) matrix of gene expression programs (GEPs) and a (N x K) matrix specifying the usage of each program for each cell in the data.

r-databaselinke-r 1.7.0-1.cf3d6cc
Propagated dependencies: r-readwriter@1.5.3-1.91373c4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/vertesy/DatabaseLinke.R
Licenses: GPL 3
Build system: r
Synopsis: Parse links to databases from your list of gene symbols
Description:

This package provides a set of functions to parse and open (search query) links to genomics related and other websites for R. Useful when you want to explore e.g.: the function of a set of differentially expressed genes.

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.

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Total results: 69112