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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-pybbi 0.4.1
Dependencies: libpng@1.6.39 openssl@3.0.8 zlib@1.3.1
Propagated dependencies: python-numpy@1.26.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/nvictus/pybbi
Licenses: Expat
Synopsis: Python bindings to UCSC Big Binary file library
Description:

This package provides Python bindings to the UCSC Big Binary (bigWig/bigBed) file library. This provides read-level access to local and remote bigWig and bigBed files but no write capabilitites. The main feature is fast retrieval of range queries into numpy arrays.

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@3.11.11 r-base64url@1.4 r-data-table@1.17.4 r-deconvr@1.14.0 r-dplyr@1.1.4 r-dt@0.33 r-ggplot2@3.5.2 r-htmltools@0.5.8.1 r-jsonlite@2.0.0 r-knitr@1.50 r-magrittr@2.0.3 r-mass@7.3-65 r-minimal@4.5.0 r-plotly@4.10.4 r-qpcr@1.4-1 r-r-utils@2.13.0 r-reshape2@1.4.4 r-rmarkdown@2.29 r-stringr@1.5.1 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+
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.

r-circus 0.1.7
Propagated dependencies: r-annotationdbi@1.70.0 r-annotationhub@3.16.0 r-biocgenerics@0.54.0 r-biomart@2.64.0 r-data-table@1.17.4 r-dbi@1.2.3 r-genomeinfodb@1.44.0 r-genomicfeatures@1.60.0 r-genomicranges@1.60.0 r-ggplot2@3.5.2 r-hash@2.2.6.3 r-iranges@2.42.0 r-rcolorbrewer@1.1-3 r-rmysql@0.11.1 r-rtracklayer@1.68.0 r-s4vectors@0.46.0 r-stringr@1.5.1 r-summarizedexperiment@1.38.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/BIMSBbioinfo/ciRcus
Licenses: Artistic License 2.0
Synopsis: Annotation, analysis and visualization of circRNA data
Description:

Circus is an R package for annotation, analysis and visualization of circRNA data. Users can annotate their circRNA candidates with host genes, gene features they are spliced from, and discriminate between known and yet unknown splice junctions. Circular-to-linear ratios of circRNAs can be calculated, and a number of descriptive plots easily generated.

r-bseqsc 1.0-1.fef3f3e
Propagated dependencies: r-abind@1.4-8 r-annotationdbi@1.70.0 r-biobase@2.68.0 r-cssam@1.4-1.9ec58c9 r-dplyr@1.1.4 r-e1071@1.7-16 r-edger@4.6.2 r-ggplot2@3.5.2 r-nmf@0.28 r-openxlsx@4.2.8 r-pkgmaker@0.32.10 r-plyr@1.8.9 r-preprocesscore@1.70.0 r-rngtools@1.5.2 r-scales@1.4.0 r-stringr@1.5.1 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+
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.

mosaik 2.2.30
Dependencies: perl@5.36.0 zlib@1.3.1 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/wanpinglee/MOSAIK
Licenses: GPL 2+ Public Domain
Synopsis: Map nucleotide sequence reads to reference genomes
Description:

MOSAIK is a program for mapping second and third-generation sequencing reads to a reference genome. MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT.

r-ewastools 1.7.2-1.f7646ca
Propagated dependencies: r-data-table@1.17.4 r-igraph@2.1.4 r-illuminaio@0.50.0 r-mblm@0.12.1 r-quadprog@1.5-8
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/hhhh5/ewastools/
Licenses: Unlicense
Synopsis: Quality control toolset for the Illumina Infinium DNA methylation
Description:

This package provides a collection of useful functions for working with DNA methylation micro-array data.

java-picard 2.10.3
Propagated dependencies: java-htsjdk@2.10.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://broadinstitute.github.io/picard/
Licenses: Expat
Synopsis: Tools for manipulating high-throughput sequencing data and formats
Description:

Picard is a set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats. Picard is implemented using the HTSJDK Java library to support accessing file formats that are commonly used for high-throughput sequencing data such as SAM, BAM, CRAM and VCF.

jellyfish 2.3.0
Dependencies: htslib@1.21
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://www.genome.umd.edu/jellyfish.html
Licenses: GPL 3+ Modified BSD
Synopsis: Tool for fast counting of k-mers in DNA
Description:

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. Jellyfish is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in a binary format, which can be translated into a human-readable text format using the jellyfish dump command, or queried for specific k-mers with jellyfish query.

r-rhtslib12 1.23.2-1.ee186da
Propagated dependencies: curl@8.6.0 zlib@1.3.1 r-zlibbioc@1.54.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/haizi-zh/Rhtslib12
Licenses: LGPL 2.0+
Synopsis: HTSlib high-throughput sequencing library as an R package
Description:

This package provides version 1.12 of the HTSlib C library for high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib.

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+
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-scdesign2 1.0.0-1.554f2c4
Propagated dependencies: r-mass@7.3-65 r-pscl@1.5.9
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/JSB-UCLA/scDesign2
Licenses: Expat
Synopsis: Statistical simulator for scRNA-seq with gene correlation
Description:

This package offers a flexible statistical simulator for scRNA-seq data. It can generate data that captures gene correlation. Additionally, it allows for varying the number of cells and sequencing depth.

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
Synopsis: Pipeline for spatial mapping of unique transcripts
Description:

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

r-wasabi 1.0.1-1.8c33cab
Propagated dependencies: r-data-table@1.17.4 r-rhdf5@2.52.0 r-rjson@0.2.23
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/COMBINE-lab/wasabi
Licenses: Modified BSD
Synopsis: Use Sailfish and Salmon with Sleuth
Description:

This package converts the output of the Sailfish and Salmon RNA-seq quantification tools so that it can be used with the Sleuth differential analysis package.

trf 4.09.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/Benson-Genomics-Lab/TRF
Licenses: AGPL 3+
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-cell2cell 0.7.4
Propagated dependencies: python-gseapy@1.0.4 python-kneed@0.8.5 python-matplotlib@3.8.2 python-networkx@3.4.2 python-numpy@1.26.4 python-openpyxl@3.1.5 python-pandas@2.2.3 python-scikit-learn@1.7.0 python-scipy@1.12.0 python-seaborn@0.13.2 python-statsmodels@0.14.4 python-scanpy@1.11.2 python-seaborn@0.13.2 python-tensorly@0.9.0 python-tqdm@4.67.1 python-umap-learn@0.5.9 python-xlrd@2.0.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/earmingol/cell2cell
Licenses: Modified BSD
Synopsis: Python library for cell communication analysis
Description:

Cell2cell is a Python library for cell communication analysis. This is a method to calculate, visualize and analyze communication between cell types. Cell2cell is suitable for single-cell RNA sequencing (scRNA-seq) data.

pigx 0.0.3
Dependencies: python@3.11.11 pigx-bsseq@0.1.10 pigx-chipseq@0.1.0 pigx-rnaseq@0.1.1 pigx-scrnaseq@1.1.10
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://bioinformatics.mdc-berlin.de/pigx/
Licenses: GPL 3+
Synopsis: Analysis pipelines for genomics
Description:

PiGx is a collection of genomics pipelines. It includes the following pipelines:

  • PiGx BSseq for raw fastq read data of bisulfite experiments

  • PiGx RNAseq for RNAseq samples

  • PiGx scRNAseq for single cell dropseq analysis

  • PiGx ChIPseq for reads from ChIPseq experiments

All pipelines are easily configured with a simple sample sheet and a descriptive settings file. The result is a set of comprehensive, interactive HTML reports with interesting findings about your samples.

r-omnipathr 3.15.3
Propagated dependencies: r-checkmate@2.3.2 r-crayon@1.5.3 r-curl@6.2.3 r-digest@0.6.37 r-dplyr@1.1.4 r-fs@1.6.6 r-httr2@1.1.2 r-igraph@2.1.4 r-jsonlite@2.0.0 r-later@1.4.2 r-logger@0.4.0 r-lubridate@1.9.4 r-magrittr@2.0.3 r-progress@1.2.3 r-purrr@1.0.4 r-r-utils@2.13.0 r-rappdirs@0.3.3 r-readr@2.1.5 r-readxl@1.4.5 r-rlang@1.1.6 r-rmarkdown@2.29 r-rsqlite@2.3.11 r-rvest@1.0.5 r-sessioninfo@1.2.3 r-stringi@1.8.7 r-stringr@1.5.1 r-tibble@3.2.1 r-tidyr@1.3.1 r-tidyselect@1.2.1 r-vctrs@0.6.5 r-withr@3.0.2 r-xml@3.99-0.18 r-xml2@1.4.0 r-yaml@2.3.10 r-zip@2.3.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/saezlab/omnipathr
Licenses: Expat
Synopsis: OmniPath web service client and more
Description:

This package provides a client for the OmniPath web service and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data, and its R implementation nichenetr.

flash 1.2.11
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://ccb.jhu.edu/software/FLASH/
Licenses: GPL 3+
Synopsis: Merge paired-end nucleotide reads from NGS experiments
Description:

FLASH (Fast Length Adjustment of SHort reads) is a tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data.

python-decoupler-py 2.1.1
Propagated dependencies: python-adjusttext@1.3.0 python-anndata@0.12.1 python-dcor@0.6 python-docrep@0.3.2 python-igraph@0.11.8 python-ipywidgets@8.1.2 python-marsilea@0.5.4 python-numba@0.61.0 python-requests@2.32.5 python-scipy@1.12.0 python-session-info2@0.2 python-tqdm@4.67.1 python-xgboost@1.7.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/scverse/decoupler
Licenses: Modified BSD
Synopsis: Framework for modeling, analyzing and interpreting single-cell RNA-seq data
Description:

This package provides different statistical methods to extract biological activities from omics data within a unified framework.

sjcount 3.2-1.292d391
Dependencies: samtools@0.1.19 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/pervouchine/sjcount-full/
Licenses: GPL 3+
Synopsis: Annotation-agnostic splice junction counting pipeline
Description:

Sjcount is a utility for fast quantification of splice junctions in RNA-seq data. It is annotation-agnostic and offset-aware. This version does count multisplits.

rscape 2.0.0.q
Propagated dependencies: gsl@2.8 openmpi@4.1.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/EddyRivasLab/R-scape
Licenses: Modified BSD
Synopsis: RNA structural covariation above phylogenetic expectation
Description:

R-scape discovers RNA secondary structure consensus elements. These elements include riboswitches and ribozymes. It utilizes probabilistic modeling of sequence alignments, explicitly considering folding dependencies. The tool enables the de novo search for new structural elements and facilitates comparative analysis of known RNA families.

python-bx-python 0.14.0
Dependencies: zlib@1.3.1
Propagated dependencies: python-numpy@1.26.4 python-pyparsing@3.2.3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/bxlab/bx-python
Licenses: Expat
Synopsis: Tools for manipulating biological data
Description:

bx-python provides tools for manipulating biological data, particularly multiple sequence alignments.

express 1.5.3
Dependencies: boost@1.83.0 bamtools@2.5.2 protobuf@3.21.9 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://bio.math.berkeley.edu/eXpress
Licenses: Artistic License 2.0
Synopsis: Streaming quantification for high-throughput genomic sequencing
Description:

eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Example applications include transcript-level RNA-Seq quantification, allele-specific/haplotype expression analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data.

lofreq 2.1.5
Dependencies: htslib@1.21 python-wrapper@3.11.11 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://csb5.github.io/lofreq/
Licenses: Expat
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.

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Total results: 45109