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

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.


r-azimuth 0.5.0-1.243ee5d
Propagated dependencies: r-bsgenome-hsapiens-ucsc-hg38@1.4.5 r-dt@0.33 r-ensdb-hsapiens-v86@2.99.0 r-future@1.49.0 r-ggplot2@3.5.2 r-glmgampoi@1.20.0 r-googlesheets4@1.1.1 r-hdf5r@1.3.12 r-htmltools@0.5.8.1 r-httr@1.4.7 r-jaspar2020@0.99.10 r-jsonlite@2.0.0 r-matrix@1.7-3 r-patchwork@1.3.0 r-plotly@4.10.4 r-presto@1.0.0-1.7636b3d r-rcpp@1.0.14 r-rlang@1.1.6 r-scales@1.4.0 r-seurat@5.3.0 r-seuratdata@0.2.2.9001-1.4dc08e0 r-seuratdisk@0.0.0.9021-1.877d4e1 r-seuratobject@5.1.0 r-shiny@1.10.0 r-shinybs@0.61.1 r-shinydashboard@0.7.3 r-shinyjs@2.1.0 r-signac@1.12.0-1.8ecdde2 r-stringr@1.5.1 r-tfbstools@1.46.0 r-withr@3.0.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/satijalab/azimuth
Licenses: GPL 3
Synopsis: Shiny app showcasing a single-cell data query-reference mapping algorithm
Description:

Azimuth utilizes an annotated reference dataset. It automates the processing, analysis, and interpretation. This applies specifically to new single-cell RNA-seq or ATAC-seq experiments. Azimuth leverages a reference-based mapping pipeline that inputs accounts matrix and performs normalization, visualization, cell annotation, and differential expression.

bbmap 39.01
Dependencies: gawk@5.3.0 java-eclipse-jdt-core@3.16.0 java-eclipse-jdt-compiler-apt@1.3.400 java-openmpi@4.1.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://sourceforge.net/projects/bbmap/
Licenses: Modified BSD
Synopsis: Aligner and other tools for short sequencing reads
Description:

This package provides bioinformatic tools to align, deduplicate, reformat, filter and normalize DNA and RNA-seq data. It includes the following tools: BBMap, a short read aligner for DNA and RNA-seq data; BBNorm, a kmer-based error-correction and normalization tool; Dedupe, a tool to simplify assemblies by removing duplicate or contained subsequences that share a target percent identity; Reformat, to convert reads between fasta/fastq/scarf/fasta+qual/sam, interleaved/paired, and ASCII-33/64, at over 500 MB/s; and BBDuk, a tool to filter, trim, or mask reads with kmer matches to an artifact/contaminant file.

megahit 1.2.9
Dependencies: python-wrapper@3.11.11 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
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.

r-cssam 1.4-1.9ec58c9
Propagated dependencies: r-formula@1.2-5 r-ggplot2@3.5.2 r-pkgmaker@0.32.10 r-plyr@1.8.9 r-rngtools@1.5.2 r-scales@1.4.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/shenorrLab/csSAM/
Licenses: LGPL 2.1+
Synopsis: Cell type-specific statistical analysis of microarray
Description:

This package implements the method csSAM that computes cell-specific differential expression from measured cell proportions using SAM.

r-dtmm 0.1.0-1.3a553b1
Propagated dependencies: r-ape@5.8-1 r-rcpp@1.0.14 r-rcpparmadillo@14.4.3-1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/MaStatLab/DTMM
Licenses: CC0
Synopsis: Dirichlet-tree multinomial mixtures
Description:

This package lets you perform unsupervised clustering of amplicon sequencing data in microbiome studies with the Dirichlet-tree Multinomial Mixtures.

java-biojava-alignment 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-biojava-phylo@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+
Synopsis: Biojava API for genetic sequence alignment
Description:

The alignment module of BioJava provides an API that contains

  • implementations of dynamic programming algorithms for sequence alignment;

  • reading and writing of popular alignment file formats;

  • a single-, or multi- threaded multiple sequence alignment algorithm.

python-peaks2utr 1.4.1
Propagated dependencies: python-asgiref@3.8.1 python-gffutils@0.13 python-importlib-resources@6.5.2 macs@2.2.9.1 python-numpy@1.26.4 python-psutil@7.0.0 python-pybedtools@0.10.0 python-pysam@0.23.0 python-requests@2.32.5 python-tqdm@4.67.1 python-typing-extensions@4.15.0 python-zipp@3.23.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/haessar/peaks2utr
Licenses: GPL 3+
Synopsis: Python CLI for annotating three prime UTR
Description:

This package provides a robust, parallelized Python CLI for annotating three prime UTR.

r-pando 1.0.5
Propagated dependencies: r-bayestestr@0.16.0 r-foreach@1.5.2 r-genomicranges@1.60.0 r-ggplot2@3.5.2 r-ggpointdensity@0.2.0 r-ggraph@2.2.1 r-glmnetutils@1.1.9 r-grr@0.9.5 r-iranges@2.42.0 r-irlba@2.3.5.1 r-matrix@1.7-3 r-matrixgenerics@1.20.0 r-motifmatchr@1.30.0 r-pals@1.10 r-patchwork@1.3.0 r-seurat@5.3.0 r-signac@1.12.0-1.8ecdde2 r-sparsematrixstats@1.20.0 r-tfbstools@1.46.0 r-tidygraph@1.3.1 r-tidyverse@2.0.0 r-uwot@0.2.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/quadbiolab/Pando
Licenses: Expat
Synopsis: Infer regulomes from multi-modal single-cell genomics data
Description:

Pando leverages multi-modal single-cell measurements to infer gene regulatory networks using a flexible linear model-based framework. By modeling the relationship between TF-binding site pairs with the expression of target genes, Pando simultaneously infers gene modules and sets of regulatory regions for each transcription factor.

velvet 1.2.10
Dependencies: openmpi@4.1.6 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.ebi.ac.uk/~zerbino/velvet/
Licenses: GPL 2+
Synopsis: Nucleic acid sequence assembler for very short reads
Description:

Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454. Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired read information, if available, to retrieve the repeated areas between contigs.

r-demultiplex2 1.0.2-2.c1ce09e
Propagated dependencies: r-data-table@1.17.4 r-devtools@2.4.5 r-dplyr@1.1.4 r-ggextra@0.10.1 r-ggplot2@3.5.2 r-gridextra@2.3 r-magrittr@2.0.3 r-mass@7.3-65 r-matrix@1.7-3 r-rcolorbrewer@1.1-3 r-shortread@1.66.0 r-stringdist@0.9.15 r-tidyr@1.3.1 r-uwot@0.2.3 r-viridis@0.6.5 r-xvector@0.48.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/Gartner-Lab/deMULTIplex2
Licenses: CC0
Synopsis: Robust sample demultiplexing for scRNA-seq
Description:

This package implements a bioinformatics algorithm for demultiplexing multiplexed single cell datasets. It is built on a statistical model of tag read counts derived from the physical mechanism of tag cross-contamination.

vbz-compression 1.0.13
Dependencies: zstd@1.5.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/nanoporetech/vbz_compression/
Licenses: MPL 2.0
Synopsis: VBZ compression plugin for nanopore signal data
Description:

VBZ Compression uses variable byte integer encoding to compress nanopore signal data. The performance of VBZ is achieved by taking advantage of the properties of the raw signal and therefore is most effective when applied to the signal dataset.

scregseg 0.1.3-0.78ebff8
Propagated dependencies: python-scikit-learn@1.6.1 python-scipy@1.12.0 python-numpy@1.26.4 python-hmmlearn@0.3.3 python-pandas@2.2.3 python-numba@0.61.0 python-anndata@0.12.1 python-scanpy@1.11.2 python-pybedtools@0.10.0 python-pysam@0.23.0 python-matplotlib@3.8.2 python-seaborn@0.13.2 python-coolbox@0.3.8
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/BIMSBbioinfo/scregseg
Licenses: GPL 3+
Synopsis: Single-cell regulatory landscape segmentation
Description:

Scregseg (Single-Cell REGulatory landscape SEGmentation) is a tool that facilitates the analysis of single cell ATAC-seq data by an HMM-based segmentation algorithm. Scregseg uses an HMM with Dirichlet-Multinomial emission probabilities to segment the genome either according to distinct relative cross-cell accessibility profiles or (after collapsing the single-cell tracks to pseudo-bulk tracks) to capture distinct cross-cluster accessibility profiles.

python-logomaker 0.8.7
Propagated dependencies: python-matplotlib@3.8.2 python-numpy@1.26.4 python-pandas@2.2.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/jbkinney/logomaker
Licenses: Expat
Synopsis: Package for making Sequence Logos
Description:

Logomaker is a Python package for generating publication-quality sequence logos. Logomaker can generate both standard and highly customized logos illustrating the properties of DNA, RNA, or protein sequences. Logos are rendered as vector graphics embedded within native matplotlib Axes objects, making them easy to style and incorporate into multi-panel figures.

louvain 0.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://sourceforge.net/projects/louvain/
Licenses: GPL 3+
Synopsis: Multi-criteria community detection
Description:

This package offers a set of functions to use in order to compute communities on graphs weighted or unweighted.

python-pysnptools 0.5.14
Propagated dependencies: python-bed-reader@1.0.6 python-cloudpickle@3.1.0 python-h5py@3.13.0 python-more-itertools@10.6.0 python-numpy@1.26.4 python-pandas@2.2.3 python-psutil@7.0.0 python-scipy@1.12.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://microsoftgenomics.github.io/PySnpTools/
Licenses: ASL 2.0
Synopsis: Library for reading and manipulating genetic data
Description:

PySnpTools is a library for reading and manipulating genetic data. It can, for example, efficiently read whole PLINK *.bed/bim/fam files or parts of those files. It can also efficiently manipulate ranges of integers using set operators such as union, intersection, and difference.

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+
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.

libsbml 5.20.5
Propagated dependencies: libxml2@2.14.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://sbml.org/Software/libSBML
Licenses: LGPL 2.1+
Synopsis: Process SBML files and data streams
Description:

LibSBML is a library to help you read, write, manipulate, translate, and validate SBML files and data streams. The Systems Biology Markup Language (SBML) is an interchange format for computer models of biological processes. SBML is useful for models of metabolism, cell signaling, and more. It continues to be evolved and expanded by an international community.

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
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.

r-bamutils 0.0.0.9000-2.0a7d2d9
Propagated dependencies: r-abind@1.4-8 r-biocgenerics@0.54.0 r-data-table@1.17.4 r-genomicalignments@1.44.0 r-genomicranges@1.60.0 r-gutils@0.2.0-2.fc24db6 r-rsamtools@2.24.0 r-variantannotation@1.54.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/mskilab/bamutils/
Licenses: GPL 2
Synopsis: Utility functions for manipulating BAMs
Description:

This package provides utility functions for manipulating BAM files.

seqan 3.0.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.seqan.de
Licenses: Modified BSD
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.

r-databaselinke-r 1.7.0-1.cf3d6cc
Propagated dependencies: r-readwriter@1.5.3-1.91373c4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/vertesy/DatabaseLinke.R
Licenses: GPL 3
Synopsis: Parse links to databases from your list of gene symbols
Description:

This package provides a set of functions to parse and open (search query) links to genomics related and other websites for R. Useful when you want to explore e.g.: the function of a set of differentially expressed genes.

java-forester 1.005
Propagated dependencies: java-commons-codec@1.15 java-openchart2@1.4.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://sites.google.com/site/cmzmasek/home/software/forester
Licenses: LGPL 2.1+
Synopsis: Phylogenomics libraries for Java
Description:

Forester is a collection of Java libraries for phylogenomics and evolutionary biology research. It includes support for reading, writing, and exporting phylogenetic trees.

go-github-com-biogo-biogo 1.0.4
Propagated dependencies: go-gopkg-in-check-v1@1.0.0-20201130134442-10cb98267c6c go-github-com-biogo-store@0.0.0-20201120204734-aad293a2328f go-github-com-biogo-hts@1.4.4 go-github-com-biogo-graph@0.0.0-20150317020928-057c1989faed
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/biogo/biogo
Licenses: Modified BSD
Synopsis: Bioinformatics library for Go
Description:

BĂ­ogo is a bioinformatics library for the Go language.

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
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.

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Total results: 45109