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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.


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.

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.

discrover 1.6.0
Dependencies: boost@1.89.0 cairo@1.18.4 rmath-standalone@4.5.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://dorina.mdc-berlin.de/public/rajewsky/discrover/
Licenses: GPL 3+
Build system: cmake
Synopsis: Discover discriminative nucleotide sequence motifs
Description:

Discrover is a motif discovery method to find binding sites of nucleic acid binding proteins.

python-slamdunk 0.4.3
Propagated dependencies: python-biopython@1.85 python-intervaltree@3.1.0 python-joblib@1.5.2 python-pandas@2.2.3 python-pybedtools@0.10.0 python-pysam@0.23.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://t-neumann.github.io/slamdunk/
Licenses: AGPL 3+
Build system: pyproject
Synopsis: Streamline SLAM-seq analysis with high sensitivity
Description:

SlamDunk is a fully automated tool for automated, robust, scalable and reproducible SLAMseq data analysis. Diagnostic plotting features and a MultiQC plugin will make your SLAMseq data ready for immediate QA and interpretation.

r-signac 1.12.0-1.8ecdde2
Dependencies: zlib@1.3.1
Propagated dependencies: r-biocgenerics@0.56.0 r-data-table@1.17.8 r-dplyr@1.1.4 r-fastmatch@1.1-6 r-future@1.68.0 r-future-apply@1.20.0 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-iranges@2.44.0 r-irlba@2.3.5.1 r-matrix@1.7-4 r-patchwork@1.3.2 r-pbapply@1.7-4 r-rcpp@1.1.0 r-rcpproll@0.3.1 r-rsamtools@2.26.0 r-s4vectors@0.48.0 r-scales@1.4.0 r-seuratobject@5.2.0 r-stringi@1.8.7 r-tidyr@1.3.1 r-tidyselect@1.2.1 r-vctrs@0.6.5
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/timoast/signac/
Licenses: Expat
Build system: r
Synopsis: Analysis of single-cell chromatin data
Description:

This package provides a framework for the analysis and exploration of single-cell chromatin data. The Signac package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis.

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.

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.

python-phylophlan 3.0.3
Propagated dependencies: python-biopython@1.85 python-dendropy@4.5.1 python-matplotlib@3.8.2 python-numpy@1.26.4 python-pandas@2.2.3 python-seaborn@0.13.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/biobakery/phylophlan
Licenses: Expat
Build system: pyproject
Synopsis: Phylogenetic analysis of microbial isolates and genomes from metagenomes
Description:

This package is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method for large-scale microbial genome characterization and phylogenetic analysis at multiple levels of resolution. This software package can assign both genomes and MAGs to SGBs. PhyloPhlAn can reconstruct strain-level phylogenies using clade- specific maximally informative phylogenetic markers, and can also scale to very large phylogenies comprising >17,000 microbial species.

r-streamgraph 0.9.0-1.76f7173
Propagated dependencies: r-dplyr@1.1.4 r-htmltools@0.5.8.1 r-htmlwidgets@1.6.4 r-magrittr@2.0.4 r-tidyr@1.3.1 r-xts@0.14.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/hrbrmstr/streamgraph
Licenses: Expat
Build system: r
Synopsis: Htmlwidget for building streamgraph visualizations
Description:

A streamgraph is a type of stacked area chart. It represents the evolution of a numeric variable for several groups. Areas are usually displayed around a central axis, and edges are rounded to give a flowing shape. This package provides an htmlwidget for building streamgraph visualizations.

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.

python-deeptoolsintervals 0.1.9
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/deeptools/deeptools_intervals
Licenses: Expat
Build system: pyproject
Synopsis: Create GTF-based interval trees with associated meta-data
Description:

This package provides a Python module creating/accessing GTF-based interval trees with associated meta-data. It is primarily used by the deeptools package.

r-gg3d 0.0.0.9000-1.ffdd837
Propagated dependencies: r-dplyr@1.1.4 r-ggplot2@4.0.1 r-magrittr@2.0.4 r-plot3d@1.4.2 r-plyr@1.8.9 r-scales@1.4.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/AckerDWM/gg3D
Licenses: GPL 3+
Build system: r
Synopsis: 3D perspective plots for ggplot2
Description:

This package adds 3D perspective plotting of points, paths, and line, 3D perspective axes, 3D perspective annotations, and wireframe plots.

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.

crossmap 0.6.1
Dependencies: python-bx-python@0.14.0 python-numpy@1.26.4 python-pybigwig@0.3.22 python-pysam@0.23.0 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://crossmap.sourceforge.net/
Licenses: GPL 2+
Build system: pyproject
Synopsis: Convert genome coordinates between assemblies
Description:

CrossMap is a program for conversion of genome coordinates or annotation files between different genome assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.

trust4 1.1.0
Dependencies: perl@5.36.0 python-wrapper@3.11.14 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/liulab-dfci/TRUST4
Licenses: GPL 3
Build system: gnu
Synopsis: TCR and BCR assembly from RNA-seq data
Description:

This package is analyzing TCR and BCR sequences using unselected RNA sequencing data, profiled from fluid and solid tissues, including tumors. TRUST4 performs de novo assembly on V, J, C genes including the hypervariable CDR3 and reports consensus contigs of BCR/TCR sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to identify the corresponding gene and CDR3 details. TRUST4 supports both single-end and paired-end bulk or single-cell sequencing data with any read length.

bustools 0.43.2
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://bustools.github.io
Licenses: FreeBSD
Build system: cmake
Synopsis: Tools for working with BUS files
Description:

bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks.

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.

r-spacexr 2.2.1-1.0a0861e
Propagated dependencies: r-compquadform@1.4.4 r-data-table@1.17.8 r-doparallel@1.0.17 r-dplyr@1.1.4 r-fields@17.1 r-foreach@1.5.2 r-ggplot2@4.0.1 r-knitr@1.50 r-locfdr@1.1-8 r-matrix@1.7-4 r-metafor@4.8-0 r-mgcv@1.9-4 r-pals@1.10 r-quadprog@1.5-8 r-readr@2.1.6 r-reshape2@1.4.5 r-rfast@2.1.5.2 r-rmarkdown@2.30 r-tibble@3.3.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/dmcable/spacexr
Licenses: GPL 3
Build system: r
Synopsis: Cell type identification and differential expression in spatial transcriptomics
Description:

This package is used for cell type identification in spatial transcriptomics. It also handles cell type-specific differential expression.

bpp-phyl 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://pbil.univ-lyon1.fr/bpp-doc/bpp-phyl/html/
Licenses: CeCILL-C
Build system: cmake
Synopsis: Bio++ phylogenetic library
Description:

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. This library provides phylogenetics-related modules.

hh-suite 3.3.0
Dependencies: openmpi@4.1.6 simde@0.8.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3019-7
Licenses: GPL 3+
Build system: cmake
Synopsis: Remote protein homology detection suite
Description:

The HH-suite is a software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).

piranha 1.2.1-1.0466d36
Dependencies: bamtools@2.5.2 samtools@0.1.19 gsl@2.8
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/smithlabcode/piranha
Licenses: GPL 3+
Build system: gnu
Synopsis: Peak-caller for CLIP-seq and RIP-seq data
Description:

Piranha is a peak-caller for genomic data produced by CLIP-seq and RIP-seq experiments. It takes input in BED or BAM format and identifies regions of statistically significant read enrichment. Additional covariates may optionally be provided to further inform the peak-calling process.

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.

r-anpan 0.3.0-1.efd4dc4
Propagated dependencies: r-ape@5.8-1 r-cli@3.6.5 r-cmdstanr@0.8.1.9000-1.a45d4f7 r-data-table@1.17.8 r-dplyr@1.1.4 r-fastglm@0.0.3 r-furrr@0.3.1 r-future@1.68.0 r-ggdendro@0.2.0 r-ggnewscale@0.5.2 r-ggplot2@4.0.1 r-loo@2.8.0 r-patchwork@1.3.2 r-phylogram@2.1.0 r-posterior@1.6.1 r-progressr@0.18.0 r-purrr@1.2.0 r-r-utils@2.13.0 r-stringr@1.6.0 r-tibble@3.3.0 r-tidyselect@1.2.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/biobakery/anpan
Licenses: Expat
Build system: r
Synopsis: Quantifying microbial strain-host associations
Description:

The goal of anpan is to consolidate statistical methods for strain analysis. This includes automated filtering of metagenomic functional profiles, testing genetic elements for association with outcomes, phylogenetic association testing, and pathway-level random effects models.

java-biojava-core 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
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://biojava.org
Licenses: LGPL 2.1+
Build system: ant
Synopsis: Core libraries of Java framework for processing biological data
Description:

BioJava is a project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.

This package provides the core libraries.

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Total results: 68658