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

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.


porechop 0.2.3-1.289d5dc
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/rrwick/porechop
Licenses: GPL 3+
Build system: pyproject
Synopsis: Finding, trimming or splitting adapters, in Oxford Nanopore reads
Description:

The porechop package is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity. Porechop also supports demultiplexing of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.

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.

lofreq 2.1.5
Dependencies: htslib@1.21 python-wrapper@3.11.14 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://csb5.github.io/lofreq/
Licenses: Expat
Build system: gnu
Synopsis: Sensitive variant calling from sequencing data
Description:

LoFreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.

hisat 0.1.6
Dependencies: perl@5.36.0 python@3.11.14 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://ccb.jhu.edu/software/hisat/index.shtml
Licenses: GPL 3+
Build system: gnu
Synopsis: Hierarchical indexing for spliced alignment of transcripts
Description:

HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads. In addition to one global FM index that represents a whole genome, HISAT uses a large set of small FM indexes that collectively cover the whole genome. These small indexes (called local indexes) combined with several alignment strategies enable effective alignment of RNA-seq reads, in particular, reads spanning multiple exons.

r-pore 0.24
Propagated dependencies: r-bit64@4.6.0-1 r-data-table@1.17.8 r-rhdf5@2.54.0 r-shiny@1.11.1 r-svdialogs@1.1.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://sourceforge.net/projects/rpore/
Licenses: Modified BSD
Build system: r
Synopsis: Visualize Nanopore sequencing data
Description:

This package provides graphical user interfaces to organize and visualize Nanopore sequencing data.

r-bseqsc 1.0-1.fef3f3e
Propagated dependencies: r-abind@1.4-8 r-annotationdbi@1.72.0 r-biobase@2.70.0 r-cssam@1.4-1.9ec58c9 r-dplyr@1.1.4 r-e1071@1.7-16 r-edger@4.8.0 r-ggplot2@4.0.1 r-nmf@0.28 r-openxlsx@4.2.8.1 r-pkgmaker@0.32.10 r-plyr@1.8.9 r-preprocesscore@1.72.0 r-rngtools@1.5.2 r-scales@1.4.0 r-stringr@1.6.0 r-xbioc@0.1.16-1.6ff0670
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/shenorrLab/bseqsc
Licenses: GPL 2+
Build system: r
Synopsis: Deconvolution of bulk sequencing experiments using single cell data
Description:

BSeq-sc is a bioinformatics analysis pipeline that leverages single-cell sequencing data to estimate cell type proportion and cell type-specific gene expression differences from RNA-seq data from bulk tissue samples. This is a companion package to the publication "A single-cell transcriptomic map of the human and mouse pancreas reveals inter- and intra-cell population structure." Baron et al. Cell Systems (2016) https://www.ncbi.nlm.nih.gov/pubmed/27667365.

python-cwl-upgrader 1.2.11
Propagated dependencies: python-ruamel.yaml@0.18.14 python-schema-salad@8.9.20250723145140
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/common-workflow-language/cwl-upgrader
Licenses: ASL 2.0
Build system: pyproject
Synopsis: CWL document upgrader
Description:

python-cwl-upgrader is a standalone upgrader for CWL documents from version draft-3, v1.0, and v1.1 to v1.2.

bwa 0.7.18
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://bio-bwa.sourceforge.net/
Licenses: GPL 3+
Build system: gnu
Synopsis: Burrows-Wheeler sequence aligner
Description:

BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.

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.

ncbi-vdb 2.10.6
Dependencies: file@5.46 hdf5@1.10.9 java-ngs@2.10.5 libxml2@2.14.6 ngs-sdk@2.10.5
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ncbi/ncbi-vdb
Licenses: Public Domain
Build system: gnu
Synopsis: Database engine for genetic information
Description:

The NCBI-VDB library implements a highly compressed columnar data warehousing engine that is most often used to store genetic information. Databases are stored in a portable image within the file system, and can be accessed/downloaded on demand across HTTP.

flexbar 3.4.0
Dependencies: tbb@2020.3 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/seqan/flexbar
Licenses: Modified BSD
Build system: cmake
Synopsis: Barcode and adapter removal tool for sequencing platforms
Description:

Flexbar preprocesses high-throughput nucleotide sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar increases read mapping rates and improves genome and transcriptome assemblies. It supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform.

r-saige 1.3.4-2.44c8dd4
Dependencies: openblas@0.3.30 plink-ng@2.0.0-a.6.16 savvy@2.1.0 superlu@5.3.0 zlib@1.3.1 zstd@1.5.6
Propagated dependencies: r-bh@1.87.0-1 r-data-table@1.17.8 r-dplyr@1.1.4 r-lintools@0.1.7 r-matrix@1.7-4 r-metaskat@0.90 r-optparse@1.7.5 r-qlcmatrix@0.9.9 r-rcpp@1.1.0 r-rcpparmadillo@15.2.2-1 r-rcppeigen@0.3.4.0.2 r-rcppparallel@5.1.11-1 r-rhpcblasctl@0.23-42 r-rsqlite@2.4.4 r-skat@2.2.5 r-spatest@3.1.2 r-survival@3.8-3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/saigegit/SAIGE
Licenses: GPL 2+
Build system: r
Synopsis: Genome-wide association tests in large-scale data sets
Description:

SAIGE is a package for efficiently controlling for case-control imbalance and sample relatedness in single-variant assoc tests (SAIGE) and controlling for sample relatedness in region-based assoc tests in large cohorts and biobanks (SAIGE-GENE+).

blast+ 2.17.0
Dependencies: bzip2@1.0.8 lmdb@0.9.29 zlib@1.3.1 pcre@8.45 perl@5.36.0 python-wrapper@3.11.14
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://blast.ncbi.nlm.nih.gov
Licenses: Public Domain Expat Boost 1.0 LGPL 2.0+ ASL 2.0
Build system: gnu
Synopsis: Basic local alignment search tool
Description:

BLAST is a popular method of performing a DNA or protein sequence similarity search, using heuristics to produce results quickly. It also calculates an “expect value” that estimates how many matches would have occurred at a given score by chance, which can aid a user in judging how much confidence to have in an alignment.

umi-tools 1.1.6
Dependencies: python-pandas@2.2.3 python-future@1.0.0 python-scipy@1.12.0 python-matplotlib@3.8.2 python-regex@2024.11.6 python-pybktree@1.1 python-scipy@1.12.0 python-pysam@0.23.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/CGATOxford/UMI-tools
Licenses: Expat
Build system: pyproject
Synopsis: Tools for analyzing unique modular identifiers
Description:

This package provides tools for dealing with Unique Molecular Identifiers (UMIs) and Random Molecular Tags (RMTs) in genetic sequences. There are six tools: the extract and whitelist commands are used to prepare a fastq containing UMIs +/- cell barcodes for alignment. The remaining commands, group, dedup, and count/count_tab, are used to identify PCR duplicates using the UMIs and perform different levels of analysis depending on the needs of the user.

python-baltica 1.1.2
Propagated dependencies: gunicorn@22.0.0 python-anndata@0.12.1 python-click@8.1.8 python-flask@3.1.0 python-flask-wtf@1.2.2 python-h5py@3.13.0 python-numpy@1.26.4 python-psutil@7.0.0 python-pysam@0.23.0 python-pyyaml@6.0.2 python-scipy@1.12.0 r-biocmanager@1.30.27 r-dplyr@1.1.4 r-genomicranges@1.62.0 r-here@1.0.2 r-openxlsx@4.2.8.1 r-optparse@1.7.5 r-readr@2.1.6 r-rsamtools@2.26.0 r-stringr@1.6.0 r-tidyr@1.3.1 r-upsetr@1.4.0 r-yaml@2.3.10 snakemake@7.32.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/dieterich-lab/Baltica
Licenses: Expat
Build system: pyproject
Synopsis: Integrated splice junction usage analysis
Description:

This framework facilitates the execution of differential junction usage (DJU) methods. Additionally, it enables the integration of results from multiple DJU methods.

r-scent 1.0.0-1.f01f18a
Dependencies: bedtools@2.31.1
Propagated dependencies: r-boot@1.3-32 r-data-table@1.17.8 r-hmisc@5.2-4 r-lme4@1.1-37 r-mass@7.3-65 r-matrix@1.7-4 r-r-utils@2.13.0 r-stringr@1.6.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/immunogenomics/SCENT
Licenses: Expat
Build system: r
Synopsis: Single-Cell enhancer target gene mapping for multimodal single-cell data
Description:

This package contains functions for the SCENT algorithm. SCENT uses single-cell multimodal data and links ATAC-seq peaks to their target genes by modeling association between chromatin accessibility and gene expression across individual single cells.

python-scdamandtools 1.0
Propagated dependencies: python-h5py@3.13.0 python-numpy@1.26.4 python-sortedcontainers@2.4.0 python-pandas@2.2.3 python-pysam@0.23.0 python-tqdm@4.67.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/KindLab/scDamAndTools
Licenses: Expat
Build system: pyproject
Synopsis: Functions for processing raw scDam&T-seq data
Description:

This is a set of functions for processing raw scDam&T-seq data. scDam&T-seq is a method to simultaneously measure protein-DNA interactions and transcription from single cells (Rooijers et al., 2019). It combines a DamID-based method to measure protein-DNA interactions and an adaptation of CEL-Seq to measure transcription. The starting point of the workflow is raw sequencing data and the end result are tables of UMI-unique DamID and CEL-Seq counts.

mosaicatcher 0.3.1
Dependencies: boost@1.89.0 htslib@1.21
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/friendsofstrandseq/mosaicatcher
Licenses: Expat
Build system: cmake
Synopsis: Count and classify Strand-seq reads
Description:

Mosaicatcher counts Strand-seq reads and classifies strand states of each chromosome in each cell using a Hidden Markov Model.

r-centipede 1.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://centipede.uchicago.edu/
Licenses: GPL 2+ GPL 3+
Build system: r
Synopsis: Predict transcription factor binding sites
Description:

CENTIPEDE applies a hierarchical Bayesian mixture model to infer regions of the genome that are bound by particular transcription factors. It starts by identifying a set of candidate binding sites, and then aims to classify the sites according to whether each site is bound or not bound by a transcription factor. CENTIPEDE is an unsupervised learning algorithm that discriminates between two different types of motif instances using as much relevant information as possible.

kentutils 302.0.0
Dependencies: zlib@1.3.1 tcsh@6.24.15 perl@5.36.0 libpng@1.6.39 mariadb@10.11.14 openssl@3.0.8
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://genome.cse.ucsc.edu/index.html
Licenses: non-copyleft
Build system: gnu
Synopsis: Assorted bioinformatics utilities
Description:

This package provides the kentUtils, a selection of bioinformatics utilities used in combination with the UCSC genome browser.

r-scenic 1.3.1-1.cedf849
Propagated dependencies: r-aucell@1.32.0 r-data-table@1.17.8 r-dynamictreecut@1.63-1 r-genie3@1.32.0 r-ggrepel@0.9.6 r-mixtools@2.0.0.1 r-nmf@0.28 r-rcistarget@1.29.0 r-rtsne@0.17
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/aertslab/SCENIC
Licenses: GPL 3
Build system: r
Synopsis: SCENIC (Single Cell rEgulatory Network Inference and Clustering)
Description:

SCENIC (Single-cell regulatory network inference and clustering) is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

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.

preseq 2.0.3
Dependencies: gsl@2.8 samtools@0.1.19 smithlab-cpp@0.1.728a097 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://smithlabresearch.org/software/preseq/
Licenses: GPL 3+
Build system: gnu
Synopsis: Program for analyzing library complexity
Description:

The preseq package is aimed at predicting and estimating the complexity of a genomic sequencing library, equivalent to predicting and estimating the number of redundant reads from a given sequencing depth and how many will be expected from additional sequencing using an initial sequencing experiment. The estimates can then be used to examine the utility of further sequencing, optimize the sequencing depth, or to screen multiple libraries to avoid low complexity samples.

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Total results: 68655