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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-celltypist 1.6.2
Propagated dependencies: python-click@8.1.8 python-leidenalg@0.10.2 python-numpy@1.26.4 python-openpyxl@3.1.5 python-pandas@2.2.3 python-scanpy@1.11.2 python-scikit-learn@1.7.0 python-requests@2.32.5
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/Teichlab/celltypist
Licenses: Expat
Build system: pyproject
Synopsis: Tool for semi-automatic cell type classification
Description:

CellTypist is an automated cell type annotation tool for scRNA-seq datasets on the basis of logistic regression classifiers optimised by the stochastic gradient descent algorithm. CellTypist allows for cell prediction using either built-in (with a current focus on immune sub-populations) or custom models, in order to assist in the accurate classification of different cell types and subtypes.

pyscenic 0.12.1-1.eaf23eb
Propagated dependencies: python-aiohttp@3.11.11 python-arboreto@0.1.6 python-attrs@25.3.0 python-boltons@25.0.0 python-cloudpickle@3.1.0 python-ctxcore@0.2.0 python-cytoolz@1.0.1 python-dask@2024.12.1 python-distributed@2024.12.1 python-frozendict@2.4.6 python-fsspec@2025.9.0 python-interlap@0.2.7 python-llvmlite@0.44.0 python-loompy@3.0.7 python-multiprocessing-on-dill@3.5.0a4 python-networkx@3.4.2 python-numba@0.61.0 python-numexpr@2.12.1 python-numpy@1.26.4 python-pandas@2.2.3 python-pyarrow@22.0.0 python-pyyaml@6.0.2 python-requests@2.32.5 python-scikit-learn@1.7.0 python-scipy@1.12.0 python-setuptools@80.9.0 python-tqdm@4.67.1 python-umap-learn@0.5.9
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://scenic.aertslab.org/
Licenses: GPL 3+
Build system: pyproject
Synopsis: Single-Cell regulatory network inference and clustering
Description:

pySCENIC is a Python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

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.

python-cooler 0.9.3
Propagated dependencies: python-asciitree@0.3.3 python-biopython@1.85 python-click@8.1.8 python-cytoolz@1.0.1 python-dask@2024.12.1 python-h5py@3.13.0 python-multiprocess@0.70.18 python-numpy@1.26.4 python-pandas@2.2.3 python-pyfaidx@0.7.2.1 python-pypairix@0.3.9 python-pysam@0.23.0 python-pyyaml@6.0.2 python-scipy@1.12.0 python-simplejson@3.20.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/open2c/cooler
Licenses: Modified BSD
Build system: pyproject
Synopsis: Sparse binary format for genomic interaction matrices
Description:

Cooler is a support library for a sparse, compressed, binary persistent storage format, called cool, used to store genomic interaction data, such as Hi-C contact matrices.

tophat 2.1.1
Dependencies: boost@1.89.0 bowtie@2.3.4.3 ncurses@6.2.20210619 perl@5.36.0 python2@2.7.18 samtools@0.1.19 seqan@1.4.2 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://ccb.jhu.edu/software/tophat/index.shtml
Licenses: Boost 1.0
Build system: gnu
Synopsis: Spliced read mapper for RNA-Seq data
Description:

TopHat is a fast splice junction mapper for nucleotide sequence reads produced by the RNA-Seq method. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

bcftools 1.21
Dependencies: gsl@2.8 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://samtools.github.io/bcftools/
Licenses: GPL 3+ Expat
Build system: gnu
Synopsis: Utilities for variant calling and manipulating VCFs and BCFs
Description:

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

python-bulkvis 2.0.0-2.00a82a9
Propagated dependencies: python-bokeh@3.7.3 python-dill@0.4.0 python-h5py@3.13.0 python-joblib@1.5.2 python-matplotlib@3.8.2 python-numpy@1.26.4 python-pandas@2.2.3 python-plotly@5.20.0 python-readpaf@0.0.10 python-scikit-learn@1.7.0 python-scikit-image@0.23.2 python-scipy@1.12.0 python-seaborn@0.13.2 python-tornado@6.4.2 python-tqdm@4.67.1 python-umap-learn@0.5.9
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/LooseLab/bulkVis
Licenses: Expat
Build system: pyproject
Synopsis: Interactive visualization of bulk RNA-seq data
Description:

This is a Python package for the interactive visualization of bulk RNA-seq data. It provides a range of plotting functions and interactive tools to explore and analyze bulk RNA-seq data.

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.

vcflib 1.0.12
Dependencies: bzip2@1.0.8 curl@8.6.0 htslib@1.21 fastahack@1.0.0 perl@5.36.0 python@3.11.14 pybind11@2.13.6 smithwaterman@0.0.0-2.2610e25 tabixpp@1.1.2 xz@5.4.5 zlib@1.3.1
Propagated dependencies: wfa2-lib@2.3.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/vcflib/vcflib/
Licenses: Expat
Build system: cmake
Synopsis: Library for parsing and manipulating VCF files
Description:

Vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. It is both an API for parsing and operating on records of genomic variation as it can be described by the VCF format, and a collection of command-line utilities for executing complex manipulations on VCF files.

vsearch 2.9.1
Dependencies: zlib@1.3.1 bzip2@1.0.8 cityhash@1.1-2.8af9b8c
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/torognes/vsearch
Licenses: GPL 3 FreeBSD
Build system: gnu
Synopsis: Sequence search tools for metagenomics
Description:

VSEARCH supports DNA sequence searching, clustering, chimera detection, dereplication, pairwise alignment, shuffling, subsampling, sorting and masking. The tool takes advantage of parallelism in the form of SIMD vectorization as well as multiple threads to perform accurate alignments at high speed. VSEARCH uses an optimal global aligner (full dynamic programming Needleman-Wunsch).

r-plsdabatch 0.2.3-1.4aadf3a
Propagated dependencies: r-ggplot2@4.0.1 r-ggpubr@0.6.2 r-gridextra@2.3 r-lmertest@3.1-3 r-mixomics@6.34.0 r-mvtnorm@1.3-3 r-performance@0.15.2 r-rdpack@2.6.4 r-scales@1.4.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/EvaYiwenWang/PLSDAbatch
Licenses: GPL 3
Build system: r
Synopsis: PLSDA-batch
Description:

This package provides a new batch effect correction method based on Projection to Latent Structures Discriminant Analysis named “PLSDA-batch” to correct data prior to any downstream analysis. PLSDA-batch estimates latent components related to treatment and batch effects to remove batch variation. The method is multivariate, non-parametric and performs dimension reduction. Combined with centered log ratio transformation for addressing uneven library sizes and compositional structure, PLSDA-batch addresses all characteristics of microbiome data that existing correction methods have ignored so far.

bpp-phyl 2.4.1
Dependencies: bpp-core@2.4.1 bpp-seq@2.4.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://pbil.univ-lyon1.fr/bpp-doc/bpp-phyl/html/
Licenses: CeCILL-C
Build system: cmake
Synopsis: Bio++ phylogenetic library
Description:

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. This library provides phylogenetics-related modules.

filtlong 0.2.0-1.d1bb46d
Dependencies: bash-minimal@5.2.37 gawk@5.3.0 python-wrapper@3.11.14 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/rrwick/Filtlong/
Licenses: GPL 3 ASL 2.0
Build system: gnu
Synopsis: Tool for quality filtering of Nanopore and PacBio data
Description:

The Filtlong package is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.

cutadapt 4.0
Dependencies: python-dnaio@0.10.0 python-xopen@1.8.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://cutadapt.readthedocs.io/en/stable/
Licenses: Expat
Build system: pyproject
Synopsis: Remove adapter sequences from nucleotide sequencing reads
Description:

Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from high-throughput sequencing reads.

r-seqgl 1.1.4
Propagated dependencies: r-biostrings@2.78.0 r-chipkernels@1.1-1.c9cfcac r-genomicranges@1.62.0 r-spams@2.6.1 r-wgcna@1.73 r-fastcluster@1.3.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ManuSetty/SeqGL
Licenses: GPL 2+
Build system: r
Synopsis: Group lasso for Dnase/ChIP-seq data
Description:

SeqGL is a group lasso based algorithm to extract transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles. This package presents a method which uses group lasso to discriminate between bound and non bound genomic regions to accurately identify transcription factors bound at the specific regions.

r-rphyloxml 0.0-9000-1.a30e392
Propagated dependencies: r-ape@5.8-1 r-xml2@1.5.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/USCbiostats/rphyloxml
Licenses: Expat
Build system: r
Synopsis: Read and write phyloXML files in R
Description:

The package reads phylogenetic data in the phyloXML format. It also includes functions for writing data in this format.

isolator 0.0.2-1.24bafc0
Dependencies: boost@1.83.0 hdf5@1.14.6 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/dcjones/isolator
Licenses: Expat
Build system: cmake
Synopsis: Tools for the analysis of RNA-Seq experiments
Description:

Isolator analyzes RNA-Seq experiments. Isolator has a particular focus on producing stable, consistent estimates. It implements a full hierarchical Bayesian model of an entire RNA-Seq experiment. It saves all the samples generated by the sampler, which can be processed to compute posterior probabilities for arbitrarily complex questions, far beyond the confines of pairwise tests. It aggressively corrects for technical effects, such as random priming bias, GC-bias, 3' bias, and fragmentation effects. Compared to other MCMC approaches, it is exceedingly efficient, though generally slower than modern maximum likelihood approaches.

r-seuratextend 1.2.5-1.5dacd7c
Propagated dependencies: r-biocmanager@1.30.27 r-dplyr@1.1.4 r-ggplot2@4.0.1 r-ggpubr@0.6.2 r-glue@1.8.0 r-hdf5r@1.3.12 r-magrittr@2.0.4 r-mosaic@1.9.2 r-purrr@1.2.0 r-remotes@2.5.0 r-reshape2@1.4.5 r-reticulate@1.44.1 r-rlist@0.4.6.2 r-scales@1.4.0 r-seurat@5.3.1 r-seuratextenddata@0.2.1-1.e7f17d4 r-seuratobject@5.2.0 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/huayc09/SeuratExtend
Licenses: GPL 3+
Build system: r
Synopsis: Enhanced toolkit for scRNA-seq analysis
Description:

This package is designed to improve and simplify the analysis of scRNA-seq data. It uses the Seurat object for this purpose. It provides an array of enhanced visualization tools, an integrated functional and pathway analysis pipeline, seamless integration with popular Python tools, and a suite of utility functions to aid in data manipulation and presentation.

sortmerna 4.3.7
Dependencies: concurrentqueue@1.0.3 gflags@2.2.2 rapidjson@1.1.0-1.949c771 rocksdb@10.4.2 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://bioinfo.lifl.fr/RNA/sortmerna/
Licenses: LGPL 3
Build system: cmake
Synopsis: Biological sequence analysis tool for NGS reads
Description:

SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU picking of NGS reads. The core algorithm is based on approximate seeds and allows for fast and sensitive analyses of nucleotide sequences. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data.

python-fcsparser 0.2.8
Propagated dependencies: python-numpy@1.26.4 python-pandas@2.2.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/eyurtsev/fcsparser
Licenses: Expat
Build system: pyproject
Synopsis: Package for reading raw fcs files
Description:

This package provides a Python package for reading raw fcs files

python-htsget 0.2.6
Propagated dependencies: python-humanize@4.14.0 python-requests@2.32.5 python-six@1.17.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://pypi.org/project/htsget/
Licenses: ASL 2.0
Build system: pyproject
Synopsis: Python API and command line interface for the GA4GH htsget API
Description:

This package is a client implementation of the GA4GH htsget protocol. It provides a simple and reliable way to retrieve genomic data from servers supporting the protocol.

r-doubletcollection 1.1.0-1.c0d62f1
Propagated dependencies: r-biocgenerics@0.56.0 r-doubletfinder@2.0.3-1.554097b r-gam@1.22-6 r-ggplot2@4.0.1 r-ggthemes@5.1.0 r-mast@1.36.0 r-mclust@6.1.2 r-prroc@1.4 r-reticulate@1.44.1 r-scales@1.4.0 r-scdblfinder@1.24.0 r-scds@1.26.0 r-seurat@5.3.1 r-singlecellexperiment@1.32.0 r-slingshot@2.18.0 r-summarizedexperiment@1.40.0 python@3.11.14 python-scrublet@0.2.3 python-doubletdetection@4.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/xnnba1984/DoubletCollection
Licenses: GPL 3+
Build system: r
Synopsis: Tool for finding doublets in scRNA-seq data
Description:

This is an R package that integrates the installation of doublet-detection methods. In addition, this tool is used for execution and benchmark of those eight mentioned methods.

java-htsjdk 2.14.3
Dependencies: java-ngs@2.10.5 java-snappy@1.0.3-rc3 java-commons-compress@1.21 java-commons-logging-minimal@1.2 java-commons-jexl@2.1.1 java-xz@1.9
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://samtools.github.io/htsjdk/
Licenses: Expat
Build system: ant
Synopsis: Java API for high-throughput sequencing data (HTS) formats
Description:

HTSJDK is an implementation of a unified Java library for accessing common file formats, such as SAM and VCF, used for high-throughput sequencing (HTS) data. There are also an number of useful utilities for manipulating HTS data.

python-deeptools 3.5.5
Propagated dependencies: python-matplotlib@3.8.2 python-numpy@1.26.4 python-numpydoc@1.5.0 python-py2bit@0.3.3 python-pybigwig@0.3.22 python-pysam@0.23.0 python-scipy@1.12.0 python-deeptoolsintervals@0.1.9 python-plotly@5.20.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://pypi.org/project/deepTools/
Licenses: Modified BSD Expat
Build system: pyproject
Synopsis: Useful tools for exploring deep sequencing data
Description:

This package addresses the challenge of handling large amounts of data that are now routinely generated from DNA sequencing centers. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files. Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome.

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