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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.


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.

r-cytonorm 0.0.10-1.166f9ff
Propagated dependencies: r-cytoml@2.22.0 r-dplyr@1.1.4 r-emdist@0.3-3 r-flowcore@2.22.0 r-flowsom@2.18.0 r-flowworkspace@4.22.0 r-ggplot2@4.0.1 r-gridextra@2.3 r-pheatmap@1.0.13 r-stringr@1.6.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/saeyslab/CytoNorm
Licenses: GPL 2+
Build system: r
Synopsis: Normalize cytometry data measured across multiple batches
Description:

This package can be used to normalize cytometry samples when a control sample is taken along in each of the batches. This is done by first identifying multiple clusters/cell types, learning the batch effects from the control samples and applying quantile normalization on all markers of interest.

python-pybedtools 0.10.0
Dependencies: zlib@1.3.1
Propagated dependencies: bedtools@2.31.1 samtools@1.19 kentutils@302.0.0 python-numpy@1.26.4 python-pandas@2.2.3 python-psutil@7.0.0 python-pysam@0.23.0 python-pyyaml@6.0.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://pythonhosted.org/pybedtools/
Licenses: Expat LGPL 2.1+
Build system: pyproject
Synopsis: Python wrapper for BEDtools programs
Description:

This package is a Python wrapper for Aaron Quinlan's BEDtools programs, which are widely used for genomic interval manipulation or "genome algebra". pybedtools extends BEDTools by offering feature-level manipulations from with Python.

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

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

python-strawc 0.0.2.1
Dependencies: curl@8.6.0 zlib@1.3.1
Propagated dependencies: pybind11@2.13.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/aidenlab/straw
Licenses: Expat
Build system: pyproject
Synopsis: Stream data from .hic files
Description:

Straw is library which allows rapid streaming of contact data from .hic files. This package provides Python bindings.

ngless 1.5.0
Dependencies: bash-minimal@5.2.37 prodigal@2.6.3 bwa@0.7.18 samtools@1.19 minimap2@2.28 megahit@1.2.9 ghc-missingh@1.5.0.1 ghc-aeson@2.0.3.0 ghc-ansi-terminal@0.11.4 ghc-async@2.2.4 ghc-atomic-write@0.2.0.7 ghc-bytestring-lexing@0.5.0.10 ghc-conduit@1.3.5 ghc-conduit-algorithms@0.0.13.0 ghc-conduit-extra@1.3.6 ghc-configurator@0.3.0.0 ghc-convertible@1.1.1.1 ghc-data-default@0.7.1.1 ghc-edit-distance@0.2.2.1 ghc-either@5.0.2 ghc-errors@2.3.0 ghc-extra@1.7.13 ghc-file-embed@0.0.15.0 ghc-filemanip@0.3.6.3 ghc-hashable@1.4.2.0 ghc-hashtables@1.3.1 ghc-hostname@1.0 ghc-http-client@0.7.13.1 ghc-http-conduit@2.3.8.1 ghc-inline-c@0.9.1.8 ghc-inline-c-cpp@0.5.0.0 ghc-int-interval-map@0.0.0.0 ghc-network@3.1.4.0 ghc-optparse-applicative@0.17.1.0 ghc-primitive@0.7.3.0 ghc-random-shuffle@0.0.4 ghc-regex@1.1.0.2 ghc-resourcet@1.2.6 ghc-safe@0.3.19 ghc-stm-chans@3.0.0.9 ghc-stm-conduit@4.0.1 ghc-strict@0.4.0.1 ghc-tar@0.5.1.1 ghc-tar-conduit@0.3.2 ghc-unix-compat@0.5.4 ghc-unliftio@0.2.25.0 ghc-unliftio-core@0.2.1.0 ghc-vector@0.12.3.1 ghc-vector-algorithms@0.8.0.4 ghc-yaml@0.11.11.1 ghc-zlib@0.6.3.0 ghc-bzlib-conduit@0.3.0.2 ghc-double-conversion@2.0.4.2 ghc-safeio@0.0.5.0
Propagated dependencies: r-r6@2.6.1 r-hdf5r@1.3.12 r-iterators@1.0.14 r-itertools@0.1-3 r-matrix@1.7-4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://ngless.embl.de/
Licenses: Expat
Build system: haskell
Synopsis: DSL for processing next-generation sequencing data
Description:

Ngless is a domain-specific language for next-generation sequencing (NGS) data processing.

python-pygam 0.9.1
Propagated dependencies: python-black@25.1.0 python-flake8@7.1.1 python-ipython@8.37.0 python-numpy@1.26.4 python-pandas@2.2.3 python-poetry-core@2.1.3 python-progressbar2@4.5.0 python-scipy@1.12.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/dswah/pyGAM
Licenses: ASL 2.0
Build system: pyproject
Synopsis: Generalized additive models in Python
Description:

This tool is for building Generalized Additive Models in Python. It emphasizes modularity and performance. The API will be immediately familiar to anyone with experience of scikit-learn or scipy.

maffilter 1.3.1
Dependencies: boost@1.89.0 bpp-core@2.4.1 bpp-phyl@2.4.1 bpp-phyl-omics@2.4.1 bpp-seq@2.4.1 bpp-seq-omics@2.4.1 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://jydu.github.io/maffilter/
Licenses: GPL 3+
Build system: cmake
Synopsis: Multiple alignment format file processor
Description:

MafFilter is a program dedicated to the analysis of genome alignments. It parses and manipulates MAF files as well as more simple fasta files. This package can be used to design a pipeline as a series of consecutive filters, each performing a dedicated analysis. Many of the filters are available, from alignment cleaning to phylogeny reconstruction and population genetics analysis. Despite various filtering options and format conversion tools, MafFilter can compute a wide range of statistics (phylogenetic trees, nucleotide diversity, inference of selection, etc.).

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.

r-chromunity 0.0.2-2.101e30a
Propagated dependencies: r-arrow@22.0.0 r-biocgenerics@0.56.0 r-bsgenome-hsapiens-ucsc-hg38@1.4.5 r-data-table@1.17.8 r-gchain@0.2.0-2.19f8bb9 r-genomicranges@1.62.0 r-gutils@0.2.0-2.fc24db6 r-igraph@2.2.1 r-magrittr@2.0.4 r-mass@7.3-65 r-matrix@1.7-4 r-pbmcapply@1.5.1 r-plyr@1.8.9 r-r6@2.6.1 r-zoo@1.8-14
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/mskilab/chromunity
Licenses: GPL 3
Build system: r
Synopsis: Discovery of communities in Pore-C concatemers
Description:

This is a package for the discovery of communities in Pore-C concatemers.

java-ngs 2.10.5
Dependencies: icedtea@3.19.0 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: Java bindings for NGS SDK
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.

r-maxprobes 0.0.2-1.c2120db
Propagated dependencies: r-minfi@1.56.0 r-minfidata@0.56.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/markgene/maxprobes
Licenses: GPL 2+
Build system: r
Synopsis: Methylation array cross-reactive probes
Description:

The Maxprobes package collects cross-reactive probes of Illumina methylation array 450K and EPIC/850K.

bless 1p02
Dependencies: openmpi@4.1.6 boost@1.83.0 sparsehash@2.0.4 pigz@2.8 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://sourceforge.net/p/bless-ec/wiki/Home/
Licenses: GPL 3+
Build system: gnu
Synopsis: Bloom-filter-based error correction tool for NGS reads
Description:

Bloom-filter-based error correction solution for high-throughput sequencing reads (BLESS) uses a single minimum-sized bloom filter is a correction tool for genomic reads produced by Next-generation sequencing (NGS). BLESS produces accurate correction results with much less memory compared with previous solutions and is also able to tolerate a higher false-positive rate. BLESS can extend reads like DNA assemblers to correct errors at the end of reads.

smithwaterman 0.0.0-2.2610e25
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ekg/smithwaterman
Licenses: GPL 2 Expat
Build system: gnu
Synopsis: Implementation of the Smith-Waterman algorithm
Description:

Implementation of the Smith-Waterman algorithm.

python-pdbfixer 1.9
Propagated dependencies: openmm@8.3.1 python-numpy@1.26.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/openmm/pdbfixer
Licenses: Expat
Build system: pyproject
Synopsis: Application for fixing problems in Protein Data Bank
Description:

PDBFixer is designed to rectify issues in Protein Data Bank files. Its intuitive interface simplifies the process of resolving problems encountered in PDB files prior to simulation tasks.

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.

genrich 0.5
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/jsh58/Genrich
Licenses: Expat
Build system: gnu
Synopsis: Detecting sites of genomic enrichment
Description:

Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). It analyzes alignment files generated following the assay and produces a file detailing peaks of significant enrichment.

fastp 0.23.2
Dependencies: isa-l@2.31.1 libdeflate@1.19
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/OpenGene/fastp/
Licenses: Expat
Build system: gnu
Synopsis: All-in-one FastQ preprocessor
Description:

Fastp is a tool designed to provide fast all-in-one preprocessing for FastQ files. This tool has multi-threading support to afford high performance.

wfmash 0.21.0
Dependencies: atomic-queue@1.6.5 gsl@2.8 htslib@1.21 libdeflate@1.19 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/waveygang/wfmash
Licenses: Expat
Build system: cmake
Synopsis: Base-accurate DNA sequence aligner
Description:

wfmash is a DNA sequence read mapper based on mash distances and the wavefront alignment algorithm. It is a fork of MashMap that implements base-level alignment via the wflign tiled wavefront global alignment algorithm. It completes MashMap with a high-performance alignment module capable of computing base-level alignments for very large sequences.

python-gffutils 0.13
Propagated dependencies: python-argcomplete@3.6.2 python-argh@0.31.3 python-biopython@1.85 python-pybedtools@0.10.0 python-pyfaidx@0.7.2.1 python-simplejson@3.20.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/daler/gffutils
Licenses: Expat
Build system: pyproject
Synopsis: Tool for manipulation of GFF and GTF files
Description:

python-gffutils is a Python package for working with and manipulating the GFF and GTF format files typically used for genomic annotations. The files are loaded into a SQLite database, allowing much more complex manipulation of hierarchical features (e.g., genes, transcripts, and exons) than is possible with plain-text methods alone.

metal 2011-03-25
Dependencies: zlib@1.3.1 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://csg.sph.umich.edu/abecasis/Metal/
Licenses: Modified BSD
Build system: gnu
Synopsis: Facilitate meta-analysis of large datasets
Description:

METAL is a tool for meta-analysis genomewide association scans. METAL can combine either test statistics and standard errors or p-values across studies (taking sample size and direction of effect into account). METAL analysis is a convenient alternative to a direct analysis of merged data from multiple studies. It is especially appropriate when data from the individual studies cannot be analyzed together because of differences in ethnicity, phenotype distribution, gender or constraints in sharing of individual level data imposed. Meta-analysis results in little or no loss of efficiency compared to analysis of a combined dataset including data from all individual studies.

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.

ensembl-vep 112
Dependencies: bioperl-minimal@1.7.0 perl-bio-db-hts@3.01 perl-dbi@1.643 perl-dbd-mysql@4.050 perl-libwww@6.78 perl-list-moreutils@0.430 perl-http-tiny@0.076 perl-json@4.02 which@2.21
Propagated dependencies: kentutils@302.0.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://www.ensembl.org/vep
Licenses: ASL 2.0
Build system: gnu
Synopsis: Predict functional effects of genomic variants
Description:

This package provides a Variant Effect Predictor, which predicts the functional effects of genomic variants. It also provides Haplosaurus, which uses phased genotype data to predict whole-transcript haplotype sequences, and Variant Recoder, which translates between different variant encodings.

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