_            _    _        _         _
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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.


perl-cworld-dekker 1.01
Dependencies: gd@2.3.3 perl-gd@2.78 bedtools@2.31.1 python-wrapper@3.11.14 python-scipy@1.12.0 python-numpy@1.26.4 python-matplotlib@3.8.2 python-h5py@3.13.0 python-scikit-learn@1.7.0 r-minimal@4.5.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/dekkerlab/cworld-dekker
Licenses: ASL 2.0
Build system: perl
Synopsis: Utility and analysis scripts for 3C, 4C, 5C, and Hi-C data
Description:

This package is a collection of Perl, Python, and R scripts for manipulating 3C/4C/5C/Hi-C data.

bio-blastxmlparser 2.0.4
Dependencies: ruby-rspec@3.13.1
Propagated dependencies: ruby-bio-logger@1.0.1 ruby-nokogiri@1.18.10
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/pjotrp/blastxmlparser
Licenses: Expat
Build system: ruby
Synopsis: Fast big data BLAST XML parser and library
Description:

Very fast parallel big-data BLAST XML file parser which can be used as command line utility. Use blastxmlparser to: Parse BLAST XML; filter output; generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.

r-demuxmix 1.1.1-1.09a7918
Propagated dependencies: r-ggplot2@4.0.1 r-gridextra@2.3 r-mass@7.3-65 r-matrix@1.7-4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/huklein/demuxmix
Licenses: Artistic License 2.0
Build system: r
Synopsis: Demultiplexing oligo-barcoded scRNA-seq data using regression mixture models
Description:

This package is used for demultiplexing single-cell sequencing experiments of pooled cells. These cells are labeled with barcode oligonucleotides. The package implements methods to fit regression mixture models for a probabilistic classification of cells, including multiplet detection. Demultiplexing error rates can be estimated, and methods for quality control are provided.

go-github-com-biogo-store 0.0.0-20201120204734-aad293a2328f
Propagated dependencies: go-gopkg-in-check-v1@1.0.0-20201130134442-10cb98267c6c go-github-com-kr-pretty@0.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/biogo/store
Licenses: Modified BSD
Build system: go
Synopsis: Interval store type for biogo
Description:

The store package provides a number of data store types that are useful for bioinformatic analysis.

htscodecs 1.6.1
Dependencies: bzip2@1.0.8 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/samtools/htscodecs
Licenses: Public Domain Modified BSD
Build system: gnu
Synopsis: Custom compression for CRAM and others
Description:

This package implements the custom CRAM codecs used for "EXTERNAL" block types. These consist of two variants of the rANS codec (8-bit and 16-bit renormalisation, with run-length encoding and bit-packing also supported in the latter), a dynamic arithmetic coder, and custom codecs for name/ID compression and quality score compression derived from fqzcomp.

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.

python-ctxcore 0.2.0
Propagated dependencies: python-cytoolz@1.0.1 python-frozendict@2.4.6 python-numba@0.61.0 python-numpy@1.26.4 python-pandas@2.2.3 python-pyarrow@22.0.0 python-pyyaml@6.0.2 python-tqdm@4.67.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/aertslab/ctxcore
Licenses: GPL 3+
Build system: pyproject
Synopsis: Core functions for pycisTarget and the SCENIC tool suite
Description:

ctxcore is part of the SCENIC suite of tools. It provides core functions for pycisTarget and SCENIC.

r-zarrarray 1.0-1.508d871
Propagated dependencies: r-biocgenerics@0.56.0 r-delayedarray@0.36.0 r-iranges@2.44.0 r-matrix@1.7-4 r-pizzarr@0.1.0-1.7b3fd72 r-s4arrays@1.10.0 r-s4vectors@0.48.0 r-sparsearray@1.10.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/BIMSBbioinfo/ZarrArray
Licenses: Expat
Build system: r
Synopsis: Zarr backend for DelayedArray objects
Description:

Zarr backend for DelayedArray objects.

python-baltica 1.1.2
Propagated dependencies: gunicorn@22.0.0 python-anndata@0.12.1 python-click@8.1.8 python-flask@3.1.0 python-flask-wtf@1.2.2 python-h5py@3.13.0 python-numpy@1.26.4 python-psutil@7.0.0 python-pysam@0.23.0 python-pyyaml@6.0.2 python-scipy@1.12.0 r-biocmanager@1.30.27 r-dplyr@1.1.4 r-genomicranges@1.62.0 r-here@1.0.2 r-openxlsx@4.2.8.1 r-optparse@1.7.5 r-readr@2.1.6 r-rsamtools@2.26.0 r-stringr@1.6.0 r-tidyr@1.3.1 r-upsetr@1.4.0 r-yaml@2.3.10 snakemake@7.32.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/dieterich-lab/Baltica
Licenses: Expat
Build system: pyproject
Synopsis: Integrated splice junction usage analysis
Description:

This framework facilitates the execution of differential junction usage (DJU) methods. Additionally, it enables the integration of results from multiple DJU methods.

r-pairwiseadonis 0.4.1-1.cb190f7
Propagated dependencies: r-cluster@2.1.8.1 r-permute@0.9-8 r-vegan@2.7-2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/pmartinezarbizu/pairwiseAdonis
Licenses: GPL 2+
Build system: r
Synopsis: Pairwise multilevel comparison using adonis
Description:

This package implements two functions:

  • pairwise.adonis is a wrapper function for multilevel pairwise comparison using adonis2 from package vegan. The function returns adjusted p-values using p.adjust(). It does not accept interaction between factors neither strata.

  • pairwise.adonis2 accepts a model formula like in adonis from vegan. You can use interactions between factors and define strata to constrain permutations. For pairwise comparison a list of unique pairwise combination of factors is produced.

skewer 0-1.978e8e4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/relipmoc/skewer
Licenses: Expat
Build system: gnu
Synopsis: Bit-masked k-difference matching
Description:

Skewer implements the bit-masked k-difference matching algorithm dedicated to the task of adapter trimming and it is specially designed for processing next-generation sequencing (NGS) paired-end sequences.

python-demuxem 0.1.7
Propagated dependencies: python-docopt@0.6.2 python-importlib-metadata@8.7.0 python-numpy@1.26.4 python-pandas@2.2.3 python-pegasusio@0.9.1 python-scikit-learn@1.7.0 python-scipy@1.12.0 python-seaborn@0.13.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/lilab-bcb/demuxEM
Licenses: Modified BSD
Build system: pyproject
Synopsis: Analyze cell-hashing/nucleus-hashing data
Description:

This is a Python module for analyzing cell-hashing/nucleus-hashing data. It is the demultiplexing module of Pegasus, which is used by Cumulus in the demultiplexing step.

r-cssam 1.4-1.9ec58c9
Propagated dependencies: r-formula@1.2-5 r-ggplot2@4.0.1 r-pkgmaker@0.32.10 r-plyr@1.8.9 r-rngtools@1.5.2 r-scales@1.4.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/shenorrLab/csSAM/
Licenses: LGPL 2.1+
Build system: r
Synopsis: Cell type-specific statistical analysis of microarray
Description:

This package implements the method csSAM that computes cell-specific differential expression from measured cell proportions using SAM.

bppsuite 2.4.1
Dependencies: bpp-core@2.4.1 bpp-seq@2.4.1 bpp-phyl@2.4.1 bpp-popgen@2.4.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/BioPP
Licenses: CeCILL-C
Build system: cmake
Synopsis: Bioinformatics tools written with the Bio++ libraries
Description:

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. This package provides command line tools using the Bio++ library.

python-pyrodigal 3.6.3
Propagated dependencies: python-archspec@0.2.5
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/althonos/pyrodigal
Licenses: GPL 3
Build system: pyproject
Synopsis: Cython bindings and Python interface for Prodigal
Description:

This package offers Cython bindings and a Python interface for Prodigal. Prodigal is an ORF finder designed for both genomes and metagenomes.

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.

ncbi-vdb 2.10.6
Dependencies: file@5.46 hdf5@1.10.9 java-ngs@2.10.5 libxml2@2.14.6 ngs-sdk@2.10.5
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ncbi/ncbi-vdb
Licenses: Public Domain
Build system: gnu
Synopsis: Database engine for genetic information
Description:

The NCBI-VDB library implements a highly compressed columnar data warehousing engine that is most often used to store genetic information. Databases are stored in a portable image within the file system, and can be accessed/downloaded on demand across HTTP.

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.

r-sleuth 0.30.1
Propagated dependencies: r-aggregation@1.0.1 r-data-table@1.17.8 r-dplyr@1.1.4 r-ggplot2@4.0.1 r-lazyeval@0.2.2 r-matrixstats@1.5.0 r-pheatmap@1.0.13 r-reshape2@1.4.5 r-rhdf5@2.54.0 r-shiny@1.11.1 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/pachterlab/sleuth
Licenses: GPL 3
Build system: r
Synopsis: Tools for investigating RNA-Seq
Description:

Sleuth is a program for differential analysis of RNA-Seq data. It makes use of quantification uncertainty estimates obtained via Kallisto for accurate differential analysis of isoforms or genes, allows testing in the context of experiments with complex designs, and supports interactive exploratory data analysis via sleuth live.

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.

bwa-pssm 0.5.11
Dependencies: gdsl@1.8 zlib@1.3.1 perl@5.36.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/pkerpedjiev/bwa-pssm
Licenses: GPL 3+
Build system: gnu
Synopsis: Burrows-Wheeler transform-based probabilistic short read mapper
Description:

BWA-PSSM is a probabilistic short genomic sequence read aligner based on the use of position specific scoring matrices (PSSM). Like many of the existing aligners it is fast and sensitive. Unlike most other aligners, however, it is also adaptible in the sense that one can direct the alignment based on known biases within the data set. It is coded as a modification of the original BWA alignment program and shares the genome index structure as well as many of the command line options.

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.

python-pairtools 1.1.0-fix
Propagated dependencies: htslib@1.21 samtools@1.19 lz4@1.10.0 python-bioframe@0.6.4 python-click@8.1.8 python-numpy@1.26.4 python-pandas@2.2.3 python-pysam@0.23.0 python-pyyaml@6.0.2 python-scipy@1.12.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/open2c/pairtools
Licenses: Expat
Build system: pyproject
Synopsis: Process mapped Hi-C data
Description:

Pairtools is a simple and fast command-line framework to process sequencing data from a Hi-C experiment. Process pair-end sequence alignments and perform the following operations:

  • detect ligation junctions (a.k.a. Hi-C pairs) in aligned paired-end sequences of Hi-C DNA molecules

  • sort .pairs files for downstream analyses

  • detect, tag and remove PCR/optical duplicates

  • generate extensive statistics of Hi-C datasets

  • select Hi-C pairs given flexibly defined criteria

  • restore .sam alignments from Hi-C pairs.

ngs-sdk 2.10.5
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ncbi/ngs
Licenses: Public Domain
Build system: gnu
Synopsis: API for accessing Next Generation Sequencing data
Description:

NGS is a domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. The API itself is independent from any particular back-end implementation, and supports use of multiple back-ends simultaneously.

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Total results: 68658