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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.


star 2.7.3a
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.

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.

libmaus2 2.0.786
Propagated dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://gitlab.com/german.tischler/libmaus2
Licenses: GPL 2+ GPL 3+
Build system: gnu
Synopsis: Collection of data structures and algorithms useful for bioinformatics
Description:

libmaus2 is a collection of data structures and algorithms. It contains:

  • I/O classes (single byte and UTF-8);

  • bitio classes (input, output and various forms of bit level manipulation);

  • text indexing classes (suffix and LCP array, fulltext and minute (FM), etc.);

  • BAM sequence alignment files input/output (simple and collating); and many lower level support classes.

tbsp 1.0.0-2.dc30c03
Dependencies: python-matplotlib@3.8.2 python-networkx@3.4.2 python-numpy@1.26.4 python-pybigwig@0.3.22 python-biopython@1.73 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/phoenixding/tbsp/
Licenses: Expat
Build system: pyproject
Synopsis: SNP-based trajectory inference
Description:

Several studies focus on the inference of developmental and response trajectories from single cell RNA-Seq (scRNA-Seq) data. A number of computational methods, often referred to as pseudo-time ordering, have been developed for this task. CRISPR has also been used to reconstruct lineage trees by inserting random mutations. The tbsp package implements an alternative method to detect significant, cell type specific sequence mutations from scRNA-Seq data.

r-projectils 3.0.0-1.cc73b97
Propagated dependencies: r-biocneighbors@2.4.0 r-biocparallel@1.44.0 r-dplyr@1.1.4 r-ggplot2@4.0.1 r-matrix@1.7-4 r-patchwork@1.3.2 r-pheatmap@1.0.13 r-pracma@2.4.6 r-purrr@1.2.0 r-rcolorbrewer@1.1-3 r-reshape2@1.4.5 r-scales@1.4.0 r-scgate@1.7.2 r-seurat@5.3.1 r-seuratobject@5.2.0 r-stacas@2.2.0 r-ucell@2.14.0 r-umap@0.2.10.0 r-uwot@0.2.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/carmonalab/ProjecTILs
Licenses: GPL 3
Build system: r
Synopsis: Reference-based analysis of scRNA-seq data
Description:

This package implements methods to project single-cell RNA-seq data onto a reference atlas, enabling interpretation of unknown cell transcriptomic states in the the context of known, reference states.

bpp-seq-omics 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://github.com/BioPP/bpp-seq-omics
Licenses: CeCILL
Build system: cmake
Synopsis: Bio++ sequence library genomics components
Description:

This library contains the genomics components of the Bio++ sequence library. It is part of the Bio++ project.

r-copykat 1.0.8-0.256de33
Propagated dependencies: r-cluster@2.1.8.1 r-dlm@1.1-6.1 r-gplots@3.2.0 r-mcmcpack@1.7-1 r-mixtools@2.0.0.1 r-paralleldist@0.2.7 r-rcolorbrewer@1.1-3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/navinlabcode/copykat
Licenses: GPL 2
Build system: r
Synopsis: Inference of genomic copy number from single cell RNAseq data
Description:

This package Copynumber KAryotyping of Tumors infers genomic copy number and subclonal structure of human tumors using integrative Bayesian approaches to identify genome-wide aneuploidy at 5MB resolution in single cells data. It separates tumor cells and tumor subclones from normal cells using high-throughput sc-RNAseq data.

proteinortho 6.3.2
Dependencies: bash-minimal@5.2.37 guile@3.0.9 diamond@2.1.6 perl@5.36.0 python-wrapper@3.11.14 blast+@2.17.0 openblas@0.3.30
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.bioinf.uni-leipzig.de/Software/proteinortho
Licenses: GPL 3+
Build system: gnu
Synopsis: Detect orthologous genes across species
Description:

Proteinortho is a tool to detect orthologous genes across different species. For doing so, it compares similarities of given gene sequences and clusters them to find significant groups. The algorithm was designed to handle large-scale data and can be applied to hundreds of species at once.

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.

r-umi4cpackage 0.0.1-1.88b07d8
Dependencies: perl@5.36.0 bowtie@2.3.4.3
Propagated dependencies: r-misha@4.1.0 r-zoo@1.8-14
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/tanaylab/umi4cpackage
Licenses: Expat
Build system: r
Synopsis: Processing and analysis of UMI-4C contact profiles
Description:

This is a package that lets you process UMI-4C data from scratch to produce nice plots.

libbigwig 0.4.4
Dependencies: zlib@1.3.1 curl@8.6.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/dpryan79/libBigWig
Licenses: Expat
Build system: gnu
Synopsis: C library for handling bigWig files
Description:

This package provides a C library for parsing local and remote BigWig files.

transanno 0.4.5
Dependencies: xz@5.4.5 zstd@1.5.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/informationsea/transanno
Licenses: GPL 3+
Build system: cargo
Synopsis: LiftOver tool for new genome assemblies
Description:

This package provides an accurate VCF/GFF3/GTF LiftOver tool for new genome assemblies.

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-taggd 0.4.0
Propagated dependencies: python-numpy@1.26.4 python-pysam@0.23.0 python-tqdm@4.67.1 python-aiofiles@24.1.0 python-dnaio@0.10.0 python-types-aiofiles@25.1.0.20251011 python-types-tqdm@4.67.0.20250809
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/jfnavarro/taggd
Licenses: Modified BSD
Build system: pyproject
Synopsis: Genetic barcode demultiplexing
Description:

This package provides TagGD barcode demultiplexing utilities for Spatial Transcriptomics data.

savvy 2.1.0
Dependencies: htslib@1.21
Propagated dependencies: streambuf-shrinkwrap@1.2.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/statgen/savvy/
Licenses: MPL 2.0
Build system: cmake
Synopsis: Interface to various variant calling formats
Description:

Savvy is the official C++ interface for the SAV file format and offers seamless support for BCF and VCF files.

r-tsis 0.2.0-1.2446029
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/wyguo/TSIS
Licenses: GPL 3
Build system: r
Synopsis: Time-series isoform switch of alternative splicing
Description:

TSIS is used for detecting transcript isoform switches in time-series data. Transcript isoform switches occur when a pair of alternatively spliced isoforms reverse the order of their relative expression levels. TSIS characterizes the transcript switch by defining the isoform switch time-points for any pair of transcript isoforms within a gene. In addition, this tool describes the switch using five different features or metrics. Also it filters the results with user’s specifications and visualizes the results using different plots for the user to examine further details of the switches.

randfold 2.0.1
Dependencies: eddylab-squid@1.9g
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/
Licenses: GPL 2
Build system: gnu
Synopsis: Minimum free energy of folding randomization test software
Description:

randfold computes the probability that, for a given sequence, the Minimum Free Energy (MFE) of the secondary structure is different from MFE computed with random sequences.

r-illuminahumanmethylationepicanno-ilm10b5-hg38 0.0.1-1.3db0691
Propagated dependencies: r-minfi@1.56.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/achilleasNP/IlluminaHumanMethylationEPICanno.ilm10b5.hg38
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illumina Human Methylation EPIC Annotation version 1.0B5
Description:

This package provides a companion annotation file to the IlluminaHumanMethylationEPICmanifest package based on the same annotation 1.0B5.

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.

instrain 1.10.0-0.6180be7
Propagated dependencies: python-biopython@1.73 python-h5py@3.13.0 python-lmfit@1.3.4 python-matplotlib@3.8.2 python-networkx@3.4.2 python-numpy@1.26.4 python-pandas@2.2.3 python-psutil@7.0.0 python-pysam@0.23.0 python-seaborn@0.13.2 python-tqdm@4.67.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/MrOlm/inStrain
Licenses: Expat
Build system: pyproject
Synopsis: Calculation of strain-level metrics
Description:

inStrain is a Python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification.

sylamer 18-131
Dependencies: gsl@2.8 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.ebi.ac.uk/research/enright/software/sylamer
Licenses: GPL 3+
Build system: gnu
Synopsis: Asses microRNA binding and siRNA off-target effects
Description:

Sylamer is a system for finding significantly over or under-represented words in sequences according to a sorted gene list. Typically it is used to find significant enrichment or depletion of microRNA or siRNA seed sequences from microarray expression data. Sylamer is extremely fast and can be applied to genome-wide datasets with ease. Results are plotted in terms of a significance landscape plot. These plots show significance profiles for each word studied across the sorted genelist.

edirect 13.3.20200128
Dependencies: bash-minimal@5.2.37 edirect-go-programs@13.3.20200128 perl-html-parser@3.72 perl-encode-locale@1.05 perl-file-listing@6.15 perl-html-tagset@3.20 perl-html-tree@5.07 perl-http-cookies@6.10 perl-http-date@6.05 perl-http-message@6.37 perl-http-negotiate@6.01 perl-lwp-mediatypes@6.04 perl-lwp-protocol-https@6.09 perl-net-http@6.22 perl-uri@5.05 perl-www-robotrules@6.02 perl-xml-simple@2.25 perl@5.36.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.ncbi.nlm.nih.gov/books/NBK179288/
Licenses: Public Domain
Build system: perl
Synopsis: Tools for accessing the NCBI's set of databases
Description:

Entrez Direct (EDirect) is a method for accessing the National Center for Biotechnology Information's (NCBI) set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a terminal. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.

EDirect also provides an argument-driven function that simplifies the extraction of data from document summaries or other results that are returned in structured XML format. This can eliminate the need for writing custom software to answer ad hoc questions.

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-pygenometracks 3.5
Propagated dependencies: python-future@1.0.0 python-gffutils@0.13 python-hicmatrix@17.1 python-intervaltree@3.1.0 python-matplotlib@3.8.2 python-numpy@1.26.4 python-pybigwig@0.3.22 python-pysam@0.23.0 python-tqdm@4.67.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://pygenometracks.readthedocs.io
Licenses: GPL 3+
Build system: pyproject
Synopsis: Program and library to plot beautiful genome browser tracks
Description:

This package aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot: bigwig, bed (many options), bedgraph, links (represented as arcs), and Hi-C matrices. pyGenomeTracks can make plots with or without Hi-C data.

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