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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.


sylamer 18-131
Dependencies: gsl@2.8 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.ebi.ac.uk/research/enright/software/sylamer
Licenses: GPL 3+
Build system: gnu
Synopsis: Asses microRNA binding and siRNA off-target effects
Description:

Sylamer is a system for finding significantly over or under-represented words in sequences according to a sorted gene list. Typically it is used to find significant enrichment or depletion of microRNA or siRNA seed sequences from microarray expression data. Sylamer is extremely fast and can be applied to genome-wide datasets with ease. Results are plotted in terms of a significance landscape plot. These plots show significance profiles for each word studied across the sorted genelist.

r-illuminahumanmethylationepicanno-ilm10b5-hg38 0.0.1-1.3db0691
Propagated dependencies: r-minfi@1.56.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/achilleasNP/IlluminaHumanMethylationEPICanno.ilm10b5.hg38
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illumina Human Methylation EPIC Annotation version 1.0B5
Description:

This package provides a companion annotation file to the IlluminaHumanMethylationEPICmanifest package based on the same annotation 1.0B5.

r-seuratextend 1.2.5-1.5dacd7c
Propagated dependencies: r-biocmanager@1.30.27 r-dplyr@1.1.4 r-ggplot2@4.0.1 r-ggpubr@0.6.2 r-glue@1.8.0 r-hdf5r@1.3.12 r-magrittr@2.0.4 r-mosaic@1.9.2 r-purrr@1.2.0 r-remotes@2.5.0 r-reshape2@1.4.5 r-reticulate@1.44.1 r-rlist@0.4.6.2 r-scales@1.4.0 r-seurat@5.3.1 r-seuratextenddata@0.2.1-1.e7f17d4 r-seuratobject@5.2.0 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/huayc09/SeuratExtend
Licenses: GPL 3+
Build system: r
Synopsis: Enhanced toolkit for scRNA-seq analysis
Description:

This package is designed to improve and simplify the analysis of scRNA-seq data. It uses the Seurat object for this purpose. It provides an array of enhanced visualization tools, an integrated functional and pathway analysis pipeline, seamless integration with popular Python tools, and a suite of utility functions to aid in data manipulation and presentation.

python-parabam 3.0.1-0.be5bd35
Propagated dependencies: python-numpy@1.26.4 python-pysam@0.23.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/cancerit/parabam
Licenses: GPL 3
Build system: pyproject
Synopsis: Parallel BAM File Analysis
Description:

Parabam is a tool for processing sequencing files in parallel. It uses Python's native multiprocessing framework to apply a user defined rule on an input file.

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-dendropy 4.5.1
Propagated dependencies: python-setuptools@80.9.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://dendropy.org/
Licenses: Modified BSD
Build system: pyproject
Synopsis: Library for phylogenetics and phylogenetic computing
Description:

DendroPy is a library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.

r-icellnet 2.2.1-1.e10ee4a
Propagated dependencies: r-annotationdbi@1.72.0 r-complexheatmap@2.26.0 r-circlize@0.4.16 r-data-table@1.17.8 r-dplyr@1.1.4 r-ggplot2@4.0.1 r-hgu133plus2-db@3.13.0 r-jetset@3.4.0 r-psych@2.5.6 r-reshape2@1.4.5 r-rlist@0.4.6.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/soumelis-lab/ICELLNET
Licenses: GPL 3
Build system: r
Synopsis: Transcriptomic-based framework to dissect cell communication
Description:

This package provides a a transcriptomic-based framework to dissect cell communication in a global manner. It integrates an original expert-curated database of ligand-receptor interactions taking into account multiple subunits expression. Based on transcriptomic profiles (gene expression), this package computes communication scores between cells and provides several visualization modes that can be helpful to dig into cell-cell interaction mechanism and extend biological knowledge.

r-psiplot 2.3.0
Propagated dependencies: r-mass@7.3-65 r-dplyr@1.1.4 r-tidyr@1.3.1 r-purrr@1.2.0 r-readr@2.1.6 r-magrittr@2.0.4 r-ggplot2@4.0.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/kcha/psiplot
Licenses: Expat
Build system: r
Synopsis: Plot percent spliced-in values of alternatively-spliced exons
Description:

PSIplot is an R package for generating plots of percent spliced-in (PSI) values of alternatively-spliced exons that were computed by vast-tools, an RNA-Seq pipeline for alternative splicing analysis. The plots are generated using ggplot2.

filevercmp 0-1.1a9b779
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ekg/filevercmp
Licenses: GPL 3+
Build system: gnu
Synopsis: This program compares version strings
Description:

This program compares version strings. It intends to be a replacement for strverscmp.

bpp-seq-omics 2.4.1
Dependencies: bpp-core@2.4.1 bpp-seq@2.4.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/BioPP/bpp-seq-omics
Licenses: CeCILL
Build system: cmake
Synopsis: Bio++ sequence library genomics components
Description:

This library contains the genomics components of the Bio++ sequence library. It is part of the Bio++ project.

fastx-toolkit 0.0.14
Dependencies: libgtextutils@0.7
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://hannonlab.cshl.edu/fastx_toolkit/
Licenses: AGPL 3+
Build system: gnu
Synopsis: Tools for FASTA/FASTQ file preprocessing
Description:

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences. The main processing of such FASTA/FASTQ files is mapping the sequences to reference genomes. However, it is sometimes more productive to preprocess the files before mapping the sequences to the genome---manipulating the sequences to produce better mapping results. The FASTX-Toolkit tools perform some of these preprocessing tasks.

r-demultiplex2 1.0.2-2.c1ce09e
Propagated dependencies: r-data-table@1.17.8 r-devtools@2.4.6 r-dplyr@1.1.4 r-ggextra@0.11.0 r-ggplot2@4.0.1 r-gridextra@2.3 r-magrittr@2.0.4 r-mass@7.3-65 r-matrix@1.7-4 r-rcolorbrewer@1.1-3 r-shortread@1.68.0 r-stringdist@0.9.15 r-tidyr@1.3.1 r-uwot@0.2.4 r-viridis@0.6.5 r-xvector@0.50.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/Gartner-Lab/deMULTIplex2
Licenses: CC0
Build system: r
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.

r-shaman 2.0-2.d6944e8
Propagated dependencies: r-data-table@1.17.8 r-domc@1.3.8 r-ggplot2@4.0.1 r-gviz@1.54.0 r-misha@4.1.0 r-plyr@1.8.9 r-rann@2.6.2 r-rcpp@1.1.0 r-reshape2@1.4.5 r-rmarkdown@2.30 r-knitr@1.50
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/tanaylab/shaman
Licenses: GPL 3+
Build system: r
Synopsis: Sampling HiC contact matrices for a-parametric normalization
Description:

The Shaman package implements functions for resampling Hi-C matrices in order to generate expected contact distributions given constraints on marginal coverage and contact-distance probability distributions. The package also provides support for visualizing normalized matrices and statistical analysis of contact distributions around selected landmarks.

r-netid 0.1.0-1.6ad1ffd
Propagated dependencies: r-doparallel@1.0.17 r-dorng@1.8.6.2 r-glmnet@4.1-10 r-hmisc@5.2-4 r-igraph@2.2.1 r-irlba@2.3.5.1 r-lmtest@0.9-40 r-matrix@1.7-4 r-mclust@6.1.2 r-pracma@2.4.6 r-raceid@0.3.9 r-rarpack@0.11-0 r-reticulate@1.44.1 r-robustrankaggreg@1.2.1 r-rsvd@1.0.5 r-seurat@5.3.1 python-anndata@0.12.1 python-geosketch@1.2 python-scanpy@1.11.2 scvelo@0.2.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/WWXkenmo/NetID_package
Licenses: Expat
Build system: r
Synopsis: Scalable method to infer fate-specific networks from single-cell data
Description:

This package provides a method to sample cells from single-cell data. It also generates an aggregate profile on a pruned K-Nearest Neighbor graph. This approach leads to an improved gene expression profile for quantifying gene regulations.

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
Build system: pyproject
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.

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-rnacrosslinkoo 0.1.3-1.a317e0f
Propagated dependencies: r-classdiscovery@3.4.9 r-doparallel@1.0.17 r-foreach@1.5.2 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-ggrepel@0.9.6 r-heatmap3@1.1.9 r-igraph@2.2.1 r-iranges@2.44.0 r-mass@7.3-65 r-mixtools@2.0.0.1 r-patchwork@1.3.2 r-r4rna@1.38.0 r-rcolorbrewer@1.1-3 r-reshape2@1.4.5 r-rrna@1.2 r-s4vectors@0.48.0 r-seqinr@4.2-36 r-tidyverse@2.0.0 r-topdom@0.10.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/cran/rnaCrosslinkOO
Licenses: GPL 3
Build system: r
Synopsis: Analysis of RNA crosslinking data
Description:

The package is ideal for analyzing RNA structure and chemical probing data.

stpipeline 2.0.0
Propagated dependencies: htseq@2.0.2 python-distance@0.1.3-0.ad7f9dc python-dnaio@0.10.0 python-numpy@1.26.4 python-pandas@2.2.3 python-pysam@0.23.0 python-regex@2024.11.6 python-scikit-learn@1.7.0 python-scipy@1.12.0 python-seaborn@0.13.2 python-taggd@0.4.0 python-types-regex@2025.9.18.20250921 samtools@1.19 star@2.7.8a
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/jfnavarro/st_pipeline
Licenses: Expat
Build system: pyproject
Synopsis: Pipeline for spatial mapping of unique transcripts
Description:

This package provides an automated pipeline for spatial mapping of unique transcripts.

ciri-long 1.0.2
Dependencies: circtools@1.0.0 python-biopython@1.85 python-bwapy@0.1.4 python-levenshtein@0.27.1 python-mappy@2.24 python-numpy@1.26.4 python-pandas@2.2.3 python-pysam@0.23.0 python-pyspoa@0.0.5 python-scikit-learn@1.7.0 python-scipy@1.12.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://ciri-cookbook.readthedocs.io/
Licenses: Expat
Build system: pyproject
Synopsis: Circular RNA identification for Nanopore sequencing
Description:

CIRI-long is a package for circular RNA identification using long-read sequencing data.

bedtools 2.18.0
Dependencies: samtools@1.19 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/arq5x/bedtools2
Licenses: Expat
Build system: gnu
Synopsis: Tools for genome analysis and arithmetic
Description:

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.

python-mygene 3.2.2
Propagated dependencies: python-biothings-client@0.2.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/biothings/mygene.py
Licenses: Modified BSD
Build system: python
Synopsis: Python Client for MyGene.Info services
Description:

MyGene.Info provides simple-to-use REST web services to query/retrieve gene annotation data. It's designed with simplicity and performance emphasized. Mygene is a Python wrapper to access MyGene.Info services.

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.

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.

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Total results: 69112