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

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.


trinityrnaseq 2.15.2
Dependencies: blast+@2.17.0 bowtie@2.3.4.3 fastqc@0.11.9 hisat@0.1.6 htslib@1.21 icedtea@3.19.0 jellyfish@2.3.0 kallisto@0.50.1 multiqc@1.14 perl@5.36.0 perl-uri-escape@1.76 python-numpy@1.26.4 python-wrapper@3.11.14 r-ape@5.8-1 r-argparse@2.3.1 r-biobase@2.70.0 r-ctc@1.84.0 r-deseq2@1.50.2 r-edger@4.8.0 r-fastcluster@1.3.0 r-glimma@2.20.0 r-goplot@1.0.2 r-goseq@1.62.0 r-gplots@3.2.0 r-minimal@4.5.2 r-qvalue@2.42.0 r-rots@2.2.0 r-sm@2.2-6.0 r-tidyverse@2.0.0 rsem@1.3.3 salmon@1.10.3 samtools@1.19 sra-tools@2.10.6 star@2.7.8a zlib@1.3.1
Propagated dependencies: coreutils@9.1 gzip@1.14 which@2.21
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/trinityrnaseq/trinityrnaseq/wiki
Licenses: Modified BSD
Build system: gnu
Synopsis: Trinity RNA-Seq de novo transcriptome assembly
Description:

Trinity assembles transcript sequences from Illumina RNA-Seq data. Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes.

scvelo 0.2.4
Propagated dependencies: pybind11@2.13.6 python-anndata@0.12.1 python-hnswlib@0.5.2 python-igraph@0.11.8 python-loompy@3.0.7 python-louvain@0.16 python-matplotlib@3.8.2 python-numba@0.61.0 python-numpy@1.26.4 python-pandas@2.2.3 python-scanpy@1.11.2 python-scikit-learn@1.7.0 python-scipy@1.12.0 python-umap-learn@0.5.9
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://scvelo.org
Licenses: Modified BSD
Build system: pyproject
Synopsis: RNA velocity generalized through dynamical modeling
Description:

ScVelo is a scalable toolkit for RNA velocity analysis in single cells. RNA velocity enables the recovery of directed dynamic information by leveraging splicing kinetics. scVelo generalizes the concept of RNA velocity by relaxing previously made assumptions with a stochastic and a dynamical model that solves the full transcriptional dynamics. It thereby adapts RNA velocity to widely varying specifications such as non-stationary populations.

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.

gffread 0.9.12-1.ba7535f
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/gpertea/gffread/
Licenses: Expat Artistic License 2.0
Build system: gnu
Synopsis: Parse and convert GFF/GTF files
Description:

This package provides a GFF/GTF file parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.

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.

star 2.7.8a
Dependencies: htslib@1.21 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/alexdobin/STAR
Licenses: GPL 3+
Build system: gnu
Synopsis: Universal RNA-seq aligner
Description:

The Spliced Transcripts Alignment to a Reference (STAR) software is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences.

cd-hit 4.8.1
Dependencies: perl@5.36.0 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://weizhongli-lab.org/cd-hit/
Licenses: GPL 2
Build system: gnu
Synopsis: Cluster and compare protein or nucleotide sequences
Description:

CD-HIT is a program for clustering and comparing protein or nucleotide sequences. CD-HIT is designed to be fast and handle extremely large databases.

r-gg3d 0.0.0.9000-1.ffdd837
Propagated dependencies: r-dplyr@1.1.4 r-ggplot2@4.0.1 r-magrittr@2.0.4 r-plot3d@1.4.2 r-plyr@1.8.9 r-scales@1.4.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/AckerDWM/gg3D
Licenses: GPL 3+
Build system: r
Synopsis: 3D perspective plots for ggplot2
Description:

This package adds 3D perspective plotting of points, paths, and line, 3D perspective axes, 3D perspective annotations, and wireframe plots.

ghc-int-interval-map 0.0.0.0
Dependencies: ghc-either@5.0.2 ghc-primitive@0.7.3.0 ghc-vector@0.12.3.1 ghc-vector-algorithms@0.8.0.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/luispedro/interval-to-int#readme
Licenses: Expat
Build system: haskell
Synopsis: Interval map structure in Haskell
Description:

An interval map structure that is optimized for low memory (each interval is represented by about 3 words + whatever the cargo is) and has semantics that are appropriate for genomic intervals (namely, intervals can overlap and queries will return all matches together). It also designed to be used in two phases: a construction phase + query phase).

samtools 1.19
Dependencies: htslib@1.21 ncurses@6.2.20210619 perl@5.36.0 python@3.11.14 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://samtools.sourceforge.net
Licenses: Expat
Build system: gnu
Synopsis: Utilities to efficiently manipulate nucleotide sequence alignments
Description:

Samtools implements various utilities for post-processing nucleotide sequence alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer.

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.

bamtools 2.5.2
Dependencies: jsoncpp@1.9.6 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/pezmaster31/bamtools
Licenses: Expat
Build system: cmake
Synopsis: C++ API and command-line toolkit for working with BAM data
Description:

BamTools provides both a C++ API and a command-line toolkit for handling BAM files.

trim-galore 0.6.6
Dependencies: gzip@1.14 perl@5.36.0 pigz@2.8 cutadapt@4.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
Licenses: GPL 3+
Build system: gnu
Synopsis: Wrapper around Cutadapt and FastQC
Description:

Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files.

segemehl 0.3.4
Dependencies: htslib@1.21 ncurses@6.2.20210619 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.bioinf.uni-leipzig.de/Software/segemehl
Licenses: GPL 3+
Build system: gnu
Synopsis: Map short sequencer reads to reference genomes
Description:

Segemehl is software to map short sequencer reads to reference genomes. Segemehl implements a matching strategy based on enhanced suffix arrays (ESA). It accepts fasta and fastq queries (gzip'ed and bgzip'ed). In addition to the alignment of reads from standard DNA- and RNA-seq protocols, it also allows the mapping of bisulfite converted reads (Lister and Cokus) and implements a split read mapping strategy. The output of segemehl is a SAM or BAM formatted alignment file.

python-pyvcf3 1.0.3-0.1fb3789
Propagated dependencies: python-setuptools@80.9.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/dridk/PyVCF3
Licenses: Expat
Build system: pyproject
Synopsis: Variant Call Format parser for Python
Description:

This package provides a VCF parser for Python.

python-pybigwig 0.3.22
Dependencies: libbigwig@0.4.4 zlib@1.3.1 curl@8.6.0
Propagated dependencies: python-numpy@1.26.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/dpryan79/pyBigWig
Licenses: Expat
Build system: pyproject
Synopsis: Access bigWig files in Python using libBigWig
Description:

This package provides Python bindings to the libBigWig library for accessing bigWig files.

megahit 1.2.9
Dependencies: python-wrapper@3.11.14 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.ncbi.nlm.nih.gov/pubmed/25609793
Licenses: GPL 3
Build system: cmake
Synopsis: Meta-genome assembler
Description:

Megahit is a fast and memory-efficient NGS assembler. It is optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single-cell assembly.

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.

newick-utils 1.6-1.da121155
Dependencies: libxml2@2.14.6 flex@2.6.4 bison@3.8.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/tjunier/newick_utils
Licenses: Modified BSD
Build system: gnu
Synopsis: Programs for working with newick format phylogenetic trees
Description:

Newick-utils is a suite of utilities for processing phylogenetic trees in Newick format. Functions include re-rooting, extracting subtrees, trimming, pruning, condensing, drawing (ASCII graphics or SVG).

nanosv 1.2.4
Dependencies: python-configparser@7.2.0 python-pysam@0.23.0 python-pyvcf3@1.0.3-0.1fb3789
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/mroosmalen/nanosv
Licenses: Expat
Build system: pyproject
Synopsis: Structural variation detection tool for Oxford Nanopore data
Description:

NanoSV is a software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies’ MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers.

java-biojava-phylo 4.2.11
Propagated dependencies: java-log4j-api@2.17.1 java-log4j-core@2.17.1 java-slf4j-api@1.7.25 java-slf4j-simple@1.7.25 java-biojava-core@4.2.11 java-forester@0-1.86b07ef
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://biojava.org
Licenses: LGPL 2.1+
Build system: ant
Synopsis: Biojava interface to the forester phylogenomics library
Description:

The phylo module provides a biojava interface layer to the forester phylogenomics library for constructing phylogenetic trees.

python-biothings-client 0.2.6
Propagated dependencies: python-requests@2.32.5
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/biothings/biothings_client.py
Licenses: Modified BSD
Build system: python
Synopsis: Python client for BioThings API services
Description:

This package provides a Python client for BioThings API services.

seqan 1.4.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.seqan.de
Licenses: Modified BSD
Build system: trivial
Synopsis: Library for nucleotide sequence analysis
Description:

SeqAn is a C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. It contains algorithms and data structures for string representation and their manipulation, online and indexed string search, efficient I/O of bioinformatics file formats, sequence alignment, and more.

python-hic2cool 1.0.1
Propagated dependencies: python-cooler@0.9.3 python-h5py@3.13.0 python-numpy@1.26.4 python-pandas@2.2.3 python-scipy@1.12.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/4dn-dcic/hic2cool
Licenses: Expat
Build system: pyproject
Synopsis: Converter for .hic and .cool files
Description:

This package provides a converter between .hic files (from juicer) and single-resolution or multi-resolution .cool files (for cooler). Both hic and cool files describe Hi-C contact matrices.

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Total results: 68655