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

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.


bedops 2.4.41
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/bedops/bedops
Licenses: GPL 2+
Build system: gnu
Synopsis: Tools for high-performance genomic feature operations
Description:

BEDOPS is a suite of tools to address common questions raised in genomic studies---mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data.

BEDOPS provides tools that perform highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.

r-ascat 2.5.2
Propagated dependencies: r-rcolorbrewer@1.1-3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/VanLoo-lab/ascat/
Licenses: GPL 3
Build system: r
Synopsis: Allele-Specific Copy Number Analysis of Tumors in R
Description:

This package provides the ASCAT R package that can be used to infer tumour purity, ploidy and allele-specific copy number profiles.

r-seuratwrappers 0.3.1-1.d28512f
Propagated dependencies: r-biocmanager@1.30.27 r-cowplot@1.2.0 r-ggplot2@4.0.1 r-igraph@2.2.1 r-matrix@1.7-4 r-remotes@2.5.0 r-rlang@1.1.6 r-rsvd@1.0.5 r-r-utils@2.13.0 r-seurat@5.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/satijalab/seurat-wrappers
Licenses: GPL 3
Build system: r
Synopsis: Community-provided methods and extensions for the Seurat object
Description:

SeuratWrappers is a collection of community-provided methods and extensions for Seurat, curated by the Satija Lab at NYGC. These methods comprise functionality not presently found in Seurat, and are able to be updated much more frequently.

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.

paml 4.9e
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://abacus.gene.ucl.ac.uk/software/paml.html
Licenses: GPL 3
Build system: gnu
Synopsis: Phylogentic analysis by maximum likelihood
Description:

PAML (for Phylogentic Analysis by Maximum Likelihood) contains a few programs for model fitting and phylogenetic tree reconstruction using nucleotide or amino-acid sequence data.

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.

r-anglemania 0.99.1-1.f27399f
Propagated dependencies: r-bigparallelr@0.3.2 r-bigstatsr@1.6.2 r-checkmate@2.3.3 r-digest@0.6.39 r-dplyr@1.1.4 r-magrittr@2.0.4 r-matrix@1.7-4 r-pbapply@1.7-4 r-rcpp@1.1.0 r-rmio@0.4.0 r-s4vectors@0.48.0 r-seurat@5.3.1 r-seuratobject@5.2.0 r-singlecellexperiment@1.32.0 r-tidyr@1.3.1 r-withr@3.0.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/BIMSBbioinfo/anglemania/
Licenses: GPL 3+
Build system: r
Synopsis: Feature extraction for scRNA-seq dataset integration
Description:

Anglemania extracts genes from multi-batch scRNA-seq experiments for downstream dataset integration. It improves conventional usage of highly-variable genes for integration tasks.

kraken2 2.1.2
Dependencies: gzip@1.14 perl@5.36.0 rsync@3.4.1 sed@4.9 wget@1.25.0 which@2.21
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/DerrickWood/kraken2
Licenses: Expat
Build system: gnu
Synopsis: Taxonomic sequence classification system
Description:

Kraken is a taxonomic sequence classifier that assigns taxonomic labels to DNA sequences. Kraken examines the k-mers within a query sequence and uses the information within those k-mers to query a database. That database maps k-mers to the lowest common ancestor (LCA) of all genomes known to contain a given k-mer.

seqtk 1.3
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/lh3/seqtk
Licenses: Expat
Build system: gnu
Synopsis: Toolkit for processing biological sequences in FASTA/Q format
Description:

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can be optionally compressed by gzip.

r-rnaseqdtu 2.0-1.5bee1e7
Propagated dependencies: r-deseq2@1.50.2 r-devtools@2.4.6 r-dexseq@1.56.0 r-drimseq@1.38.0 r-edger@4.8.0 r-rafalib@1.0.4 r-stager@1.32.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/mikelove/rnaseqDTU/
Licenses: Artistic License 2.0
Build system: r
Synopsis: RNA-seq workflow for differential transcript usage
Description:

This package provides an RNA-seq workflow for differential transcript usage (DTU) following Salmon quantification. This workflow performs a DTU analysis on simulated data. It also shows how to use stageR to perform two-stage testing of DTU, a statistical framework to screen at the gene level and then confirm which transcripts within the significant genes show evidence of DTU.

python-multivelo 0.1.2
Propagated dependencies: python-anndata@0.12.1 python-h5py@3.13.0 python-ipywidgets@8.1.2 python-joblib@1.5.2 python-loompy@3.0.7 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-seaborn@0.13.2 python-tqdm@4.67.1 python-umap-learn@0.5.9 scvelo@0.2.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/welch-lab/MultiVelo
Licenses: Modified BSD
Build system: pyproject
Synopsis: Velocity inference from single-cell multi-omic data
Description:

MultiVelo uses a probabilistic latent variable model to estimate the switch time and rate parameters of gene regulation, providing a quantitative summary of the temporal relationship between epigenomic and transcriptomic changes.

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.

rcas-web 0.1.0-2.71c93e3
Dependencies: bash-minimal@5.2.37 r-minimal@4.5.2 r-rcas@1.36.0 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+
Build system: gnu
Synopsis: Web interface for RNA-centric annotation system (RCAS)
Description:

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

r-catch 1.0-1.196ddd5
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/zhanyinx/CaTCH_R
Licenses: GPL 2+
Build system: r
Synopsis: Call a hierarchy of domains based on Hi-C data
Description:

This package allows building the hierarchy of domains starting from Hi-C data. Each hierarchical level is identified by a minimum value of physical insulation between neighboring domains.

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.

ccwl 0.4.0
Dependencies: bash-minimal@5.2.37 guile@3.0.9 guile-libyaml@1.0.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://ccwl.systemreboot.net
Licenses: GPL 3+
Build system: gnu
Synopsis: Concise common workflow language
Description:

The ccwl is a concise syntax to express CWL workflows. ccwl is a compiler to generate CWL workflows from concise descriptions in ccwl. It is implemented as an EDSL in the Scheme programming language.

macs 3.0.2
Propagated dependencies: python-cykhash@2.0.1 python-hmmlearn@0.3.3 python-numpy@1.26.4 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/macs3-project/MACS
Licenses: Modified BSD
Build system: pyproject
Synopsis: Model based analysis for ChIP-Seq data
Description:

MACS is an implementation of a ChIP-Seq analysis algorithm for identifying transcript factor binding sites named Model-based Analysis of ChIP-Seq (MACS). MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions and it improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation.

sjcount 3.2-1.292d391
Dependencies: samtools@0.1.19 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/pervouchine/sjcount-full/
Licenses: GPL 3+
Build system: gnu
Synopsis: Annotation-agnostic splice junction counting pipeline
Description:

Sjcount is a utility for fast quantification of splice junctions in RNA-seq data. It is annotation-agnostic and offset-aware. This version does count multisplits.

r-domultibarheatmap 0.1.0-1.9e65afa
Propagated dependencies: r-ggplot2@4.0.1 r-magrittr@2.0.4 r-rlang@1.1.6 r-seurat@5.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/elliefewings/DoMultiBarHeatmap
Licenses: CC0
Build system: r
Synopsis: Produce heatmap from a Seurat object with multiple annotation bars
Description:

This package builds on Seurat's Doheatmap function code to produce a heatmap from a Seurat object with multiple annotation bars.

flair 1.6.4
Dependencies: bash-minimal@5.2.37 r-minimal@4.5.2 r-apeglm@1.32.0 r-deseq2@1.50.2 r-drimseq@1.38.0 r-ggplot2@4.0.1 r-lazyeval@0.2.2 r-qqman@0.1.9 r-rlang@1.1.6
Propagated dependencies: python-mappy@2.24 python-numpy@1.26.4 python-ncls@0.0.68 python-pybedtools@0.10.0 python-pysam@0.23.0 python-rpy2@3.5.17 python-scipy@1.12.0 python-tqdm@4.67.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://flair.readthedocs.io/en/latest/
Licenses: Modified BSD
Build system: python
Synopsis: Full-length alternative isoform analysis of RNA
Description:

This package implements FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads.

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.

kallisto 0.50.1
Dependencies: hdf5@1.14.6 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://pachterlab.github.io/kallisto/
Licenses: FreeBSD
Build system: cmake
Synopsis: Near-optimal RNA-Seq quantification
Description:

Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. Pseudoalignment of reads preserves the key information needed for quantification, and kallisto is therefore not only fast, but also as accurate as existing quantification tools.

python-bulkvis 2.0.0-2.00a82a9
Propagated dependencies: python-bokeh@3.7.3 python-dill@0.4.0 python-h5py@3.13.0 python-joblib@1.5.2 python-matplotlib@3.8.2 python-numpy@1.26.4 python-pandas@2.2.3 python-plotly@5.20.0 python-readpaf@0.0.10 python-scikit-learn@1.7.0 python-scikit-image@0.23.2 python-scipy@1.12.0 python-seaborn@0.13.2 python-tornado@6.4.2 python-tqdm@4.67.1 python-umap-learn@0.5.9
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/LooseLab/bulkVis
Licenses: Expat
Build system: pyproject
Synopsis: Interactive visualization of bulk RNA-seq data
Description:

This is a Python package for the interactive visualization of bulk RNA-seq data. It provides a range of plotting functions and interactive tools to explore and analyze bulk RNA-seq data.

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Total results: 68658