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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.


python-biom-format 2.1.16
Propagated dependencies: python-anndata@0.12.1 python-click@8.1.8 python-flake8@7.1.1 python-future@1.0.0 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://www.biom-format.org
Licenses: Modified BSD
Build system: pyproject
Synopsis: Biological Observation Matrix (BIOM) format utilities
Description:

The BIOM file format is designed to be a general-use format for representing counts of observations e.g. operational taxonomic units, KEGG orthology groups or lipid types, in one or more biological samples e.g. microbiome samples, genomes, metagenomes.

r-gchain 0.2.0-2.19f8bb9
Propagated dependencies: r-bamutils@0.0.0.9000-2.0a7d2d9 r-biostrings@2.78.0 r-data-table@1.17.8 r-genomicalignments@1.46.0 r-genomicranges@1.62.0 r-gtrack@0.1.0-1.a694fa3 r-gutils@0.2.0-2.fc24db6 r-matrix@1.7-4 r-rtracklayer@1.70.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/mskilab/gChain/
Licenses: GPL 2
Build system: r
Synopsis: Additional capabilities and speed for GenomicRanges operations
Description:

This R package provides additional capabilities and speed for GenomicRanges operations.

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.

tophat 2.1.1
Dependencies: boost@1.89.0 bowtie@2.3.4.3 ncurses@6.2.20210619 perl@5.36.0 python2@2.7.18 samtools@0.1.19 seqan@1.4.2 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://ccb.jhu.edu/software/tophat/index.shtml
Licenses: Boost 1.0
Build system: gnu
Synopsis: Spliced read mapper for RNA-Seq data
Description:

TopHat is a fast splice junction mapper for nucleotide sequence reads produced by the RNA-Seq method. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

r-sigfit 2.2.0
Propagated dependencies: r-rcpp@1.1.0 r-rstan@2.32.7 r-rstantools@2.5.0 r-coda@0.19-4.1 r-clue@0.3-66 r-knitr@1.50 r-rmarkdown@2.30 r-bh@1.87.0-1 r-rcppeigen@0.3.4.0.2 r-stanheaders@2.32.10
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/kgori/sigfit
Licenses: GPL 3
Build system: r
Synopsis: Flexible Bayesian inference of mutational signatures
Description:

This R package lets you estimate signatures of mutational processes and their activities on mutation count data. Starting from a set of single-nucleotide variants (SNVs), it allows both estimation of the exposure of samples to predefined mutational signatures (including whether the signatures are present at all), and identification of signatures de novo from the mutation counts.

python-scanorama 1.7.4
Propagated dependencies: python-annoy@1.17.3 python-fbpca@1.0 python-geosketch@1.2 python-intervaltree@3.1.0 python-matplotlib@3.8.2 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/brianhie/scanorama
Licenses: Expat
Build system: pyproject
Synopsis: Panoramic stitching of heterogeneous single cell transcriptomic data
Description:

Scanorama enables batch-correction and integration of heterogeneous scRNA-seq datasets, which is described in the paper "Efficient integration of heterogeneous single-cell transcriptomes using Scanorama" by Brian Hie, Bryan Bryson, and Bonnie Berger.

python-cgatcore 0.6.16
Dependencies: time@1.9
Propagated dependencies: python-apsw@3.46.0.0 python-gevent@24.11.1 python-pandas@2.2.3 python-paramiko@4.0.0 python-pyyaml@6.0.2 python-ruffus@2.8.4 python-sqlalchemy@1.4.42
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/cgat-developers/cgat-core
Licenses: Expat
Build system: pyproject
Synopsis: Computational genomics analysis toolkit
Description:

CGAT-core is a set of libraries and helper functions used to enable researchers to design and build computational workflows for the analysis of large-scale data-analysis.

python-vireosnp 0.5.9-0.e365463
Propagated dependencies: python-matplotlib@3.8.2 python-numpy@1.26.4 python-scipy@1.12.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/huangyh09/vireoSNP
Licenses: ASL 2.0
Build system: pyproject
Synopsis: Deconvolution based on SNP for multiplexed scRNA-seq data
Description:

This package provides a deconvolution based on Single Nucleotide Position (SNP) for multiplexed scRNA-seq data. The name vireo stand for Variational Inference for Reconstructing Ensemble Origin by expressed SNPs in multiplexed scRNA-seq data and follows the clone identification from single-cell data named cardelino.

plink-ng 2.0.0-a.6.16
Dependencies: libdeflate@1.19 openblas@0.3.30 zlib@1.3.1 zstd@1.5.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.cog-genomics.org/plink/
Licenses: GPL 3+
Build system: gnu
Synopsis: Whole genome association analysis toolset
Description:

PLINK is a whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.

pigx-sars-cov2-ww 0.0.9
Dependencies: bash-minimal@5.2.37 bedtools@2.31.1 bwa@0.7.18 ensembl-vep@112 fastp@0.23.2 fastqc@0.11.9 ivar@1.4.4 kraken2@2.1.2 krona-tools@2.8 lofreq@2.1.5 multiqc@1.14 python-pyyaml@6.0.2 python-wrapper@3.11.14 r-base64url@1.4 r-data-table@1.17.8 r-deconvr@1.16.0 r-dplyr@1.1.4 r-dt@0.34.0 r-ggplot2@4.0.1 r-htmltools@0.5.8.1 r-jsonlite@2.0.0 r-knitr@1.50 r-magrittr@2.0.4 r-mass@7.3-65 r-minimal@4.5.2 r-plotly@4.11.0 r-qpcr@1.4-2 r-r-utils@2.13.0 r-reshape2@1.4.5 r-rmarkdown@2.30 r-stringr@1.6.0 r-tidyr@1.3.1 r-viridis@0.6.5 samtools@1.19 snakemake@7.32.4 wget@1.25.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://bioinformatics.mdc-berlin.de/pigx/
Licenses: GPL 3+
Build system: gnu
Synopsis: Analysis pipeline for wastewater sequencing
Description:

PiGx SARS-CoV-2 is a pipeline for analysing data from sequenced wastewater samples and identifying given variants-of-concern of SARS-CoV-2. The pipeline can be used for continuous sampling. The output report will provide an intuitive visual overview about the development of variant abundance over time and location.

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.

r-battenberg 2.2.9
Propagated dependencies: r-devtools@2.4.6 r-readr@2.1.6 r-doparallel@1.0.17 r-ggplot2@4.0.1 r-rcolorbrewer@1.1-3 r-gridextra@2.3 r-gtools@3.9.5 r-ascat@2.5.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/Wedge-lab/battenberg
Licenses: GPL 3
Build system: r
Synopsis: Subclonal copy number estimation in R
Description:

This package contains the Battenberg R package for subclonal copy number estimation, as described by Nik-Zainal et al.

python-metacells 0.9.5
Propagated dependencies: python-anndata@0.12.1 python-cvxpy@1.4.3 python-fastcluster@1.2.6 python-igraph@0.11.8 python-importlib-metadata@8.7.0 python-numpy@1.26.4 python-pandas@2.2.3 python-psutil@7.0.0 python-pyyaml@6.0.2 python-scanpy@1.11.2 python-scipy@1.12.0 python-threadpoolctl@3.1.0 python-umap-learn@0.5.9
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/tanaylab/metacells.git
Licenses: Expat
Build system: pyproject
Synopsis: Single-cell RNA Sequencing Analysis
Description:

The metacells package implements the improved metacell algorithm for single-cell RNA sequencing (scRNA-seq) data analysis within the scipy framework, and projection algorithm based on it. The original metacell algorithm was implemented in R. The Python package contains various algorithmic improvements and is scalable for larger data sets (millions of cells).

repeat-masker 4.1.2-p1
Dependencies: bash-minimal@5.2.37 perl@5.36.0 perl-text-soundex@3.05 python@3.11.14 python-h5py@3.13.0 hmmer@3.3.2 trf@4.09.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/Benson-Genomics-Lab/TRF
Licenses: The Open Software License 2.1
Build system: gnu
Synopsis: Tandem Repeats Finder: a program to analyze DNA sequences
Description:

A tandem repeat in DNA is two or more adjacent, approximate copies of a pattern of nucleotides. Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. In order to use the program, the user submits a sequence in FASTA format. The output consists of two files: a repeat table file and an alignment file. Submitted sequences may be of arbitrary length. Repeats with pattern size in the range from 1 to 2000 bases are detected.

python-pybiomart 0.2.0
Propagated dependencies: python-future@1.0.0 python-pandas@2.2.3 python-requests@2.32.5 python-requests-cache@1.2.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/jrderuiter/pybiomart
Licenses: Expat
Build system: pyproject
Synopsis: A simple pythonic interface to biomart
Description:

Pybiomart provides a simple pythonic interface to biomart.

r-bedtorch 0.1.12.12-1.f5ff4f8
Propagated dependencies: r-assertthat@0.2.1 r-curl@7.0.0 r-data-table@1.17.8 r-dplyr@1.1.4 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-purrr@1.2.0 r-r-utils@2.13.0 r-rcpp@1.1.0 r-rcurl@1.98-1.17 r-readr@2.1.6 r-rhtslib12@1.23.2-1.ee186da r-s4vectors@0.48.0 r-stringr@1.6.0 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/haizi-zh/bedtorch/
Licenses: Expat
Build system: r
Synopsis: R package for fast BED-file manipulation
Description:

The goal of bedtorch is to provide a fast BED file manipulation tool suite native in R.

r-doubletcollection 1.1.0-1.c0d62f1
Propagated dependencies: r-biocgenerics@0.56.0 r-doubletfinder@2.0.3-1.554097b r-gam@1.22-6 r-ggplot2@4.0.1 r-ggthemes@5.1.0 r-mast@1.36.0 r-mclust@6.1.2 r-prroc@1.4 r-reticulate@1.44.1 r-scales@1.4.0 r-scdblfinder@1.24.0 r-scds@1.26.0 r-seurat@5.3.1 r-singlecellexperiment@1.32.0 r-slingshot@2.18.0 r-summarizedexperiment@1.40.0 python@3.11.14 python-scrublet@0.2.3 python-doubletdetection@4.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/xnnba1984/DoubletCollection
Licenses: GPL 3+
Build system: r
Synopsis: Tool for finding doublets in scRNA-seq data
Description:

This is an R package that integrates the installation of doublet-detection methods. In addition, this tool is used for execution and benchmark of those eight mentioned methods.

bowtie1 1.3.1
Dependencies: python-wrapper@3.11.14 tbb@2021.6.0 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://bowtie-bio.sourceforge.net/index.shtml
Licenses: Artistic License 2.0
Build system: gnu
Synopsis: Fast aligner for short nucleotide sequence reads
Description:

Bowtie is a fast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

checkm 1.1.3
Dependencies: python-dendropy@4.5.1 python-matplotlib@3.8.2 python-numpy@1.26.4 python-pysam@0.23.0 python-scipy@1.12.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://ecogenomics.github.io/CheckM/
Licenses: GPL 3+
Build system: pyproject
Synopsis: Assess the quality of putative genome bins
Description:

CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. It provides robust estimates of genome completeness and contamination by using collocated sets of genes that are ubiquitous and single-copy within a phylogenetic lineage. Assessment of genome quality can also be examined using plots depicting key genomic characteristics (e.g., GC, coding density) which highlight sequences outside the expected distributions of a typical genome. CheckM also provides tools for identifying genome bins that are likely candidates for merging based on marker set compatibility, similarity in genomic characteristics, and proximity within a reference genome.

qtltools 1.3.1
Dependencies: curl@8.6.0 gsl@2.8 boost@1.89.0 rmath-standalone@4.5.2 htslib@1.3.1 openssl@3.0.8 openblas@0.3.30 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://qtltools.github.io/qtltools/
Licenses: GPL 3+
Build system: gnu
Synopsis: Tool set for molecular QTL discovery and analysis
Description:

QTLtools is a tool set for molecular QTL discovery and analysis. It allows going from the raw genetic sequence data to collection of molecular Quantitative Trait Loci (QTLs) in few easy-to-perform steps.

python-goatools 1.3.1
Propagated dependencies: python-docopt@0.6.2 python-numpy@1.26.4 python-openpyxl@3.1.5 python-pandas@2.2.3 python-pydot@4.0.1 python-requests@2.32.5 python-scipy@1.12.0 python-setuptools@80.9.0 python-statsmodels@0.14.4 python-xlsxwriter@3.2.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/tanghaibao/goatools
Licenses: FreeBSD
Build system: pyproject
Synopsis: Python scripts to find enrichment of GO terms
Description:

Python scripts to find enrichment of GO terms. In addition, this package is used for processing the obo-formatted file from Gene Ontology website. The data structure is a directed acyclic graph that allows easy traversal from leaf to root.

python-snaptools 1.4.8
Propagated dependencies: python-future@1.0.0 python-h5py@3.13.0 python-louvain@0.16 python-numpy@1.26.4 python-pybedtools@0.10.0 python-pysam@0.23.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/r3fang/SnapTools
Licenses: ASL 2.0
Build system: pyproject
Synopsis: Tools for processing snap files
Description:

SnapTools can operate on snap files the following types of operations:

  • index the reference genome before alignment;

  • align reads to the corresponding reference genome;

  • pre-process by convert pair-end reads into fragments, checking the mapping quality score, alignment and filtration;

  • create the cell-by-bin matrix.

jamm 1.0.7.6
Dependencies: bash@5.2.37 coreutils@9.1 gawk@5.3.0 perl@5.36.0 r-minimal@4.5.2 r-signal@1.8-1 r-mclust@6.1.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/mahmoudibrahim/JAMM
Licenses: GPL 3+
Build system: gnu
Synopsis: Peak finder for NGS datasets
Description:

JAMM is a peak finder for next generation sequencing datasets (ChIP-Seq, ATAC-Seq, DNase-Seq, etc.) that can integrate replicates and assign peak boundaries accurately. JAMM is applicable to both broad and narrow datasets.

methyldackel 0.6.1
Dependencies: curl@8.6.0 htslib@1.21 libbigwig@0.4.4 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/dpryan79/MethylDackel
Licenses: Expat
Build system: gnu
Synopsis: Universal methylation extractor for BS-seq experiments
Description:

MethylDackel will process a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq alignments and extract per-base methylation metrics from them. MethylDackel requires an indexed fasta file containing the reference genome as well.

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Total results: 68658