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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.


tetoolkit 2.2.3
Dependencies: bash-minimal@5.2.37 coreutils@9.1 bedtools@2.31.1 python-pysam@0.23.0 r-minimal@4.5.2 r-deseq2@1.50.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/mhammell-laboratory/TEtranscripts
Licenses: GPL 3+
Build system: pyproject
Synopsis: Transposable elements in differential enrichment analysis
Description:

This is package for including transposable elements in differential enrichment analysis of sequencing datasets. TEtranscripts and TEcount take RNA-seq (and similar data) and annotates reads to both genes and transposable elements. TEtranscripts then performs differential analysis using DESeq2. Note that TEtranscripts and TEcount rely on specially curated GTF files, which are not included due to their size.

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.

bio-blastxmlparser 2.0.4
Dependencies: ruby-rspec@3.13.1
Propagated dependencies: ruby-bio-logger@1.0.1 ruby-nokogiri@1.18.10
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/pjotrp/blastxmlparser
Licenses: Expat
Build system: ruby
Synopsis: Fast big data BLAST XML parser and library
Description:

Very fast parallel big-data BLAST XML file parser which can be used as command line utility. Use blastxmlparser to: Parse BLAST XML; filter output; generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.

r-cytonorm 0.0.10-1.166f9ff
Propagated dependencies: r-cytoml@2.22.0 r-dplyr@1.1.4 r-emdist@0.3-3 r-flowcore@2.22.0 r-flowsom@2.18.0 r-flowworkspace@4.22.0 r-ggplot2@4.0.1 r-gridextra@2.3 r-pheatmap@1.0.13 r-stringr@1.6.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/saeyslab/CytoNorm
Licenses: GPL 2+
Build system: r
Synopsis: Normalize cytometry data measured across multiple batches
Description:

This package can be used to normalize cytometry samples when a control sample is taken along in each of the batches. This is done by first identifying multiple clusters/cell types, learning the batch effects from the control samples and applying quantile normalization on all markers of interest.

bwa-pssm 0.5.11
Dependencies: gdsl@1.8 zlib@1.3.1 perl@5.36.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/pkerpedjiev/bwa-pssm
Licenses: GPL 3+
Build system: gnu
Synopsis: Burrows-Wheeler transform-based probabilistic short read mapper
Description:

BWA-PSSM is a probabilistic short genomic sequence read aligner based on the use of position specific scoring matrices (PSSM). Like many of the existing aligners it is fast and sensitive. Unlike most other aligners, however, it is also adaptible in the sense that one can direct the alignment based on known biases within the data set. It is coded as a modification of the original BWA alignment program and shares the genome index structure as well as many of the command line options.

bamutils 1.0.15
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://genome.sph.umich.edu/wiki/BamUtil
Licenses: GPL 3+
Build system: gnu
Synopsis: Programs for working on SAM/BAM files
Description:

This package provides several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable called bam.

java-biojava-alignment 4.0.0
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@4.0.0 java-biojava-phylo@4.0.0 java-forester@1.005
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://biojava.org
Licenses: LGPL 2.1+
Build system: ant
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.

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
Build system: ant
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.

adapterremoval 2.3.3
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://adapterremoval.readthedocs.io/
Licenses: GPL 3+
Build system: gnu
Synopsis: Rapid sequence adapter trimming, identification, and read merging
Description:

This program searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, the AdapterRemoval may be used to recover a consensus adapter sequence for paired-ended data, for which this information is not available.

arriba 1.0.1
Dependencies: bash-minimal@5.2.37 htslib@1.21 r-minimal@4.5.2 r-circlize@0.4.16 r-genomicalignments@1.46.0 r-genomicranges@1.62.0 samtools@1.19 star@2.7.8a zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/suhrig/arriba
Licenses: Expat GPL 3
Build system: gnu
Synopsis: Gene fusion detection from RNA-Seq data
Description:

Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for the use in a clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria. It is based on the fast STAR aligner and the post-alignment runtime is typically just around two minutes. In contrast to many other fusion detection tools which build on STAR, Arriba does not require to reduce the alignIntronMax parameter of STAR to detect small deletions.

python-changeo 1.3.4
Propagated dependencies: python-airr@1.5.1 python-biopython@1.85 python-importlib-resources@6.5.2 python-numpy@1.26.4 python-packaging@25.0 python-pandas@2.2.3 python-presto@0.7.6 python-pyyaml@6.0.2 python-scipy@1.12.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://changeo.readthedocs.io
Licenses: GPL 3
Build system: pyproject
Synopsis: Repertoire clonal assignment toolkit
Description:

Change-O is a collection of tools for processing the output of V(D)J alignment tools, assigning clonal clusters to immunoglobulin (Ig) sequences, and reconstructing germline sequences.

python-telomerecat 4.0.2
Propagated dependencies: python-click@8.1.8 python-numpy@1.26.4 python-pandas@2.2.3 python-parabam@3.0.1-0.be5bd35 python-pysam@0.23.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/cancerit/telomerecat
Licenses: GPL 3
Build system: pyproject
Synopsis: Telomere computational analysis tool
Description:

Telomerecat is a tool for estimating the average telomere length (TL) for a paired end, whole genome sequencing (WGS) sample.

Telomerecat is adaptable, accurate and fast. The algorithm accounts for sequencing amplification artifacts, anneouploidy (common in cancer samples) and noise generated by WGS. For a high coverage WGS BAM file of around 100GB telomerecat can produce an estimate in ~1 hour.

r-pairadise 1.0.0
Propagated dependencies: r-doparallel@1.0.17 r-foreach@1.5.2 r-iterators@1.0.14 r-nloptr@2.2.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/Xinglab/PAIRADISE
Licenses: Expat
Build system: r
Synopsis: Paired replicate analysis of allelic differential splicing events
Description:

PAIRADISE is a method for detecting allele-specific alternative splicing (ASAS) from RNA-seq data. Unlike conventional approaches that detect ASAS events one sample at a time, PAIRADISE aggregates ASAS signals across multiple individuals in a population. By treating the two alleles of an individual as paired, and multiple individuals sharing a heterozygous SNP as replicates, PAIRADISE formulates ASAS detection as a statistical problem for identifying differential alternative splicing from RNA-seq data with paired replicates.

r-disgenet2r 0.99.2-1.8d8ce37
Propagated dependencies: r-data-table@1.17.8 r-ggplot2@4.0.1 r-gtable@0.3.6 r-httr@1.4.7 r-igraph@2.2.1 r-jsonlite@2.0.0 r-purrr@1.2.0 r-reshape@0.8.10 r-reshape2@1.4.5 r-sparql@1.16 r-stringr@1.6.0 r-tidyr@1.3.1 r-tidyverse@2.0.0 r-venndiagram@1.7.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://bitbucket.org/ibi_group/disgenet2r
Licenses: Expat
Build system: r
Synopsis: Query, visualize, and expand DisGeNET data
Description:

This is an R package to query and expand DisGeNET data, and to visualize the results within R framework. The disgenet2r package is designed to retrieve data from DisGeNET v6.0 (Jan, 2019).

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+
Build system: pyproject
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.

r-snapatac 2.0
Propagated dependencies: r-bigmemory@4.6.4 r-doparallel@1.0.17 r-dosnow@1.0.20 r-edger@4.8.0 r-foreach@1.5.2 r-genomicranges@1.62.0 r-igraph@2.2.1 r-iranges@2.44.0 r-irlba@2.3.5.1 r-matrix@1.7-4 r-plyr@1.8.9 r-plot3d@1.4.2 r-rann@2.6.2 r-raster@3.6-32 r-rcolorbrewer@1.1-3 r-rhdf5@2.54.0 r-rtsne@0.17 r-scales@1.4.0 r-viridis@0.6.5
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/r3fang/SnapATAC
Licenses: GPL 3
Build system: r
Synopsis: Single nucleus analysis package for ATAC-Seq
Description:

This package provides a fast and accurate analysis toolkit for single cell ATAC-seq (Assay for transposase-accessible chromatin using sequencing). Single cell ATAC-seq can resolve the heterogeneity of a complex tissue and reveal cell-type specific regulatory landscapes. However, the exceeding data sparsity has posed unique challenges for the data analysis. This package r-snapatac is an end-to-end bioinformatics pipeline for analyzing large- scale single cell ATAC-seq data which includes quality control, normalization, clustering analysis, differential analysis, motif inference and exploration of single cell ATAC-seq sequencing data.

python-cooltools 0.7.0
Propagated dependencies: python-bioframe@0.6.4 python-click@8.1.8 python-cooler@0.9.3 python-joblib@1.5.2 python-matplotlib@3.8.2 python-multiprocess@0.70.18 python-numba@0.61.0 python-numpy@1.26.4 python-pandas@2.2.3 python-scikit-image@0.23.2 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/open2c/cooltools
Licenses: Expat
Build system: pyproject
Synopsis: Analysis tools for genomic interaction data stored in .cool format
Description:

This package provides necessary tools for the analysis of the genomic interaction data stored in .cool format. This collection of tools includes operations like compartment, insulation or peak calling.

python-twobitreader 3.1.9
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/benjschiller/twobitreader
Licenses: Artistic License 2.0
Build system: pyproject
Synopsis: Python library for reading .2bit files
Description:

twobitreader is a Python library for reading .2bit files as used by the UCSC genome browser.

r-genenmf 0.9.2-1.7ac4752
Propagated dependencies: r-cluster@2.1.8.1 r-colorspace@2.1-2 r-dendextend@1.19.1 r-irlba@2.3.5.1 r-lsa@0.73.3 r-matrix@1.7-4 r-pheatmap@1.0.13 r-rcppml@0.3.7 r-seurat@5.3.1 r-viridis@0.6.5
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/carmonalab/GeneNMF
Licenses: GPL 3
Build system: r
Synopsis: Non-Negative matrix factorization for single-cell omics
Description:

This package provides a collection of methods to extract gene programs from single-cell gene expression data using non-negative matrix factorization (NMF). GeneNMF contains functions to directly interact with the Seurat toolkit and derive interpretable gene program signatures.

python-strawc 0.0.2.1
Dependencies: curl@8.6.0 zlib@1.3.1
Propagated dependencies: pybind11@2.13.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/aidenlab/straw
Licenses: Expat
Build system: pyproject
Synopsis: Stream data from .hic files
Description:

Straw is library which allows rapid streaming of contact data from .hic files. This package provides Python bindings.

python-celltypist 1.6.2
Propagated dependencies: python-click@8.1.8 python-leidenalg@0.10.2 python-numpy@1.26.4 python-openpyxl@3.1.5 python-pandas@2.2.3 python-scanpy@1.11.2 python-scikit-learn@1.7.0 python-requests@2.32.5
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/Teichlab/celltypist
Licenses: Expat
Build system: pyproject
Synopsis: Tool for semi-automatic cell type classification
Description:

CellTypist is an automated cell type annotation tool for scRNA-seq datasets on the basis of logistic regression classifiers optimised by the stochastic gradient descent algorithm. CellTypist allows for cell prediction using either built-in (with a current focus on immune sub-populations) or custom models, in order to assist in the accurate classification of different cell types and subtypes.

python-cwlformat 2022.02.18
Propagated dependencies: python-importlib-resources@6.5.2 python-ruamel.yaml@0.18.14
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/rabix/cwl-format
Licenses: ASL 2.0
Build system: pyproject
Synopsis: Prettifier for CWL code
Description:

python-cwlformat is a specification and a reference implementation for a very opinionated CWL code formatter. It outputs CWL in a standardized YAML format.

circtools 1.0.0
Dependencies: bioparser@3.0.13 biosoup@0.10.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/Kevinzjy/circtools
Licenses: Expat
Build system: cargo
Synopsis: Accelerating functions in CIRI toolkit
Description:

This package provides accelerated functions for the CIRI toolkit. It also provides the ccs executable to scan for circular consensus sequences.

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