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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.


tabixpp 1.1.2
Dependencies: bzip2@1.0.8 curl@8.6.0 htslib@1.21 xz@5.4.5 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ekg/tabixpp
Licenses: Expat
Synopsis: C++ wrapper around tabix project
Description:

This is a C++ wrapper around the Tabix project which abstracts some of the details of opening and jumping in tabix-indexed files.

bio-locus 0.0.7
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/pjotrp/bio-locus
Licenses: Expat
Synopsis: Tool for fast querying of genome locations
Description:

Bio-locus is a tabix-like tool for fast querying of genome locations. Many file formats in bioinformatics contain records that start with a chromosome name and a position for a SNP, or a start-end position for indels. Bio-locus allows users to store this chr+pos or chr+pos+alt information in a database.

hisat2 2.2.1
Dependencies: python-wrapper@3.11.11
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://daehwankimlab.github.io/hisat2/
Licenses: GPL 3+
Synopsis: Graph-based alignment of genomic sequencing reads
Description:

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). In addition to using one global graph FM (GFM) index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes, combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).

python-presto 0.7.6
Propagated dependencies: muscle@3.8.1551 python-biopython@1.85 python-numpy@1.26.4 python-pandas@2.2.3 python-pyyaml@6.0.2 python-scipy@1.12.0 vsearch@2.9.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/immcantation/presto
Licenses: AGPL 3
Synopsis: The REpertoire Sequencing TOolkit
Description:

Presto is a python toolkit for processing raw reads from high-throughput sequencing of B cell and T cell repertoires.

ivar 1.4.4
Dependencies: htslib@1.21 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://andersen-lab.github.io/ivar/html/
Licenses: GPL 3+
Synopsis: Tools for amplicon-based sequencing
Description:

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

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+
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.

rcas-web 0.1.0-2.71c93e3
Dependencies: bash-minimal@5.2.37 r-minimal@4.5.0 r-rcas@1.34.0 guile@3.0.9 guile-json@4.7.3 guile-redis@2.2.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/BIMSBbioinfo/rcas-web
Licenses: AGPL 3+
Synopsis: Web interface for RNA-centric annotation system (RCAS)
Description:

This package provides a simple web interface for the RNA-centric annotation system (RCAS).

delly 0.8.3
Dependencies: boost@1.83.0 bzip2@1.0.8 htslib@1.21 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/dellytools/delly
Licenses: GPL 3+
Synopsis: Integrated structural variant prediction method
Description:

Delly is an integrated structural variant prediction method that can discover and genotype deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome.

r-stringendo 0.6.0-1.15594b1
Propagated dependencies: r-clipr@0.8.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/vertesy/Stringendo
Licenses: GPL 3
Synopsis: Stringendo is a string parsing library
Description:

This package provides string parsing functionalities for generating plotnames, filenames and paths.

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
Synopsis: Interval store type for biogo
Description:

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

phast 1.5
Dependencies: clapack@3.2.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://compgen.cshl.edu/phast/
Licenses: Modified BSD
Synopsis: Phylogenetic analysis with space/time models
Description:

Phylogenetic Analysis with Space/Time models (PHAST) is a collection of command-line programs and supporting libraries for comparative and evolutionary genomics. Best known as the search engine behind the Conservation tracks in the University of California, Santa Cruz (UCSC) Genome Browser, PHAST also includes several tools for phylogenetic modeling, functional element identification, as well as utilities for manipulating alignments, trees and genomic annotations.

r-zarrarray 1.0-1.508d871
Propagated dependencies: r-biocgenerics@0.54.0 r-delayedarray@0.34.1 r-iranges@2.42.0 r-matrix@1.7-3 r-pizzarr@0.1.0-1.7b3fd72 r-s4arrays@1.8.0 r-s4vectors@0.46.0 r-sparsearray@1.8.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/BIMSBbioinfo/ZarrArray
Licenses: Expat
Synopsis: Zarr backend for DelayedArray objects
Description:

Zarr backend for DelayedArray objects.

intervaltree 0.0.0-1.b90527f
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ekg/intervaltree
Licenses: Expat
Synopsis: Minimal C++ interval tree implementation
Description:

An interval tree can be used to efficiently find a set of numeric intervals overlapping or containing another interval. This library provides a basic implementation of an interval tree using C++ templates, allowing the insertion of arbitrary types into the tree.

python-decoupler 2.1.1
Propagated dependencies: python-adjusttext@1.3.0 python-anndata@0.12.1 python-dcor@0.6 python-docrep@0.3.2 python-igraph@0.11.8 python-ipywidgets@8.1.2 python-marsilea@0.5.4 python-numba@0.61.0 python-requests@2.32.5 python-scipy@1.12.0 python-session-info2@0.2 python-tqdm@4.67.1 python-xgboost@1.7.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/scverse/decoupler
Licenses: Modified BSD
Synopsis: Framework for modeling, analyzing and interpreting single-cell RNA-seq data
Description:

This package provides different statistical methods to extract biological activities from omics data within a unified framework.

r-premessa 0.3.4-1.68b42bb
Propagated dependencies: r-data-table@1.17.4 r-flowcore@2.20.0 r-ggplot2@3.5.2 r-gridextra@2.3 r-hexbin@1.28.5 r-jsonlite@2.0.0 r-reshape@0.8.9 r-rhandsontable@0.3.8 r-shiny@1.10.0 r-shinyjqui@0.4.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ParkerICI/premessa
Licenses: GPL 3
Synopsis: Pre-processing of flow and mass cytometry data
Description:

This is an R package for pre-processing of flow and mass cytometry data. This package includes panel editing or renaming for FCS files, bead-based normalization and debarcoding.

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
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.

r-doubletfinder 2.0.3-1.554097b
Propagated dependencies: r-fields@16.3.1 r-kernsmooth@2.23-26 r-rocr@1.0-11
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/chris-mcginnis-ucsf/DoubletFinder
Licenses: CC0
Synopsis: Identify doublets in single-cell RNA sequencing data
Description:

DoubletFinder identifies doublets by generating artificial doublets from existing scRNA-seq data and defining which real cells preferentially co-localize with artificial doublets in gene expression space. Other DoubletFinder package functions are used for fitting DoubletFinder to different scRNA-seq datasets. For example, ideal DoubletFinder performance in real-world contexts requires optimal pK selection and homotypic doublet proportion estimation. pK selection is achieved using pN-pK parameter sweeps and maxima identification in mean-variance-normalized bimodality coefficient distributions. Homotypic doublet proportion estimation is achieved by finding the sum of squared cell annotation frequencies.

r-scopeloomr 0.13.0-1.99726f5
Propagated dependencies: r-base64enc@0.1-3 r-hdf5r@1.3.12 r-igraph@2.1.4 r-matrix@1.7-3 r-plyr@1.8.9 r-rjson@0.2.23 r-rlist@0.4.6.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/aertslab/SCopeLoomR
Licenses: Expat
Synopsis: Build .loom files and extract data from them
Description:

This is an R package to build generic .loom files aligning with the default naming convention of the .loom format and to integrate other data types e.g.: regulons (SCENIC), clusters from Seurat, trajectory information... The package can also be used to extract data from .loom files.

phylip 3.697
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://evolution.genetics.washington.edu/phylip/
Licenses: FreeBSD
Synopsis: Tools for inferring phylogenies
Description:

PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees).

r-streamgraph 0.9.0-1.76f7173
Propagated dependencies: r-dplyr@1.1.4 r-htmltools@0.5.8.1 r-htmlwidgets@1.6.4 r-magrittr@2.0.3 r-tidyr@1.3.1 r-xts@0.14.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/hrbrmstr/streamgraph
Licenses: Expat
Synopsis: Htmlwidget for building streamgraph visualizations
Description:

A streamgraph is a type of stacked area chart. It represents the evolution of a numeric variable for several groups. Areas are usually displayed around a central axis, and edges are rounded to give a flowing shape. This package provides an htmlwidget for building streamgraph visualizations.

fsom 0.0.0-1.a6ef318
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ekg/fsom
Licenses: GPL 3
Synopsis: Manage SOM (Self-Organizing Maps) neural networks
Description:

A tiny C library for managing SOM (Self-Organizing Maps) neural networks.

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+
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.

samtools 0.1.19
Dependencies: htslib@1.21 ncurses@6.2.20210619 perl@5.36.0 python@3.11.11 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://samtools.sourceforge.net
Licenses: Expat
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.

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