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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.


instrain 1.10.0-0.6180be7
Propagated dependencies: python-biopython@1.73 python-h5py@3.13.0 python-lmfit@1.3.4 python-matplotlib@3.8.2 python-networkx@3.4.2 python-numpy@1.26.4 python-pandas@2.2.3 python-psutil@7.0.0 python-pysam@0.23.0 python-seaborn@0.13.2 python-tqdm@4.67.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/MrOlm/inStrain
Licenses: Expat
Build system: pyproject
Synopsis: Calculation of strain-level metrics
Description:

inStrain is a Python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification.

go-github-com-biogo-hts 1.4.4
Propagated dependencies: go-github-com-ulikunitz-xz@0.5.12 go-github-com-kortschak-utter@1.7.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/biogo/hts
Licenses: Modified BSD
Build system: go
Synopsis: HTS module for biogo
Description:

This package provides tools for handling BAM, SAM, Tabix, bgzf, CRAM, CSIv1, CSIv2 and FAI files.

r-miamiplot 1.1.0-1.beede9c
Propagated dependencies: r-checkmate@2.3.3 r-dplyr@1.1.4 r-ggplot2@4.0.1 r-ggrepel@0.9.6 r-gridextra@2.3 r-magrittr@2.0.4 r-rlang@1.1.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/juliedwhite/miamiplot
Licenses: GPL 2
Build system: r
Synopsis: Create a ggplot2 miami plot
Description:

This package generates a Miami plot with centered chromosome labels. The output is a ggplot2 object. Users can specify which data they want plotted on top vs. bottom, whether to display significance line(s), what colors to give chromosomes, and what points to label.

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.

ribotaper 1.3.1
Dependencies: bash-minimal@5.2.37 bedtools@2.18.0 samtools@0.1.19 r-minimal@4.5.2 r-foreach@1.5.2 r-xnomial@1.0.4.1 r-domc@1.3.8 r-multitaper@1.0-17 r-seqinr@4.2-36
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/
Licenses: GPL 3+
Build system: gnu
Synopsis: Define translated ORFs using ribosome profiling data
Description:

Ribotaper is a method for defining translated open reading frames (ORFs) using ribosome profiling (ribo-seq) data. This package provides the Ribotaper pipeline.

python-multivelo 0.1.2
Propagated dependencies: python-anndata@0.12.1 python-h5py@3.13.0 python-ipywidgets@8.1.2 python-joblib@1.5.2 python-loompy@3.0.7 python-matplotlib@3.8.2 python-numba@0.61.0 python-numpy@1.26.4 python-pandas@2.2.3 python-scanpy@1.11.2 python-scikit-learn@1.7.0 python-scipy@1.12.0 python-seaborn@0.13.2 python-tqdm@4.67.1 python-umap-learn@0.5.9 scvelo@0.2.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/welch-lab/MultiVelo
Licenses: Modified BSD
Build system: pyproject
Synopsis: Velocity inference from single-cell multi-omic data
Description:

MultiVelo uses a probabilistic latent variable model to estimate the switch time and rate parameters of gene regulation, providing a quantitative summary of the temporal relationship between epigenomic and transcriptomic changes.

r-singlet 0.99.26-1.765a6c4
Propagated dependencies: r-dplyr@1.1.4 r-fgsea@1.36.0 r-ggplot2@4.0.1 r-knitr@1.50 r-limma@3.66.0 r-matrix@1.7-4 r-msigdbr@25.1.1 r-rcpp@1.1.0 r-rcppml-devel@0.5.6-2.5449a5b r-reshape2@1.4.5 r-scuttle@1.20.0 r-seurat@5.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/zdebruine/singlet
Licenses: GPL 2+
Build system: r
Synopsis: Non-negative Matrix Factorization for single-cell analysis
Description:

This is a package for fast Non-negative Matrix Factorization (NMF) with automatic rank-determination for dimension reduction of single-cell data using Seurat, RcppML nmf, SingleCellExperiments and similar.

salmon 1.10.3
Dependencies: boost@1.83.0 bzip2@1.0.8 cereal@1.3.2 curl@8.6.0 eigen@3.4.0 htscodecs@1.6.1 jemalloc@5.3.0 libgff@2.0.0 tbb@2021.6.0 libstadenio@1.14.8 xz@5.4.5 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/COMBINE-lab/salmon
Licenses: GPL 3+
Build system: cmake
Synopsis: Quantification from RNA-seq reads using lightweight alignments
Description:

Salmon is a program to produce highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves its accuracy and speed via a number of different innovations, including the use of lightweight alignments (accurate but fast-to-compute proxies for traditional read alignments) and massively-parallel stochastic collapsed variational inference.

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.

bandage 0.8.1
Dependencies: qtbase@5.15.17 qtsvg@5.15.17
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://rrwick.github.io/Bandage/
Licenses: GPL 2+ GPL 3+
Build system: qt
Synopsis: Bioinformatics Application for Navigating De novo Assembly Graphs Easily
Description:

Bandage is a program for visualising de novo assembly graphs. It allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. De novo assembly graphs contain not only assembled contigs but also the connections between those contigs, which were previously not easily accessible. Bandage visualises assembly graphs, with connections, using graph layout algorithms. Nodes in the drawn graph, which represent contigs, can be automatically labelled with their ID, length or depth. Users can interact with the graph by moving, labelling and colouring nodes. Sequence information can also be extracted directly from the graph viewer. By displaying connections between contigs, Bandage opens up new possibilities for analysing and improving de novo assemblies that are not possible by looking at contigs alone.

cnvkit 0.9.12
Dependencies: r-minimal@4.5.2
Propagated dependencies: python-biopython@1.85 python-future@1.0.0 python-matplotlib@3.8.2 python-numpy@1.26.4 python-pandas@2.2.3 python-pomegranate@0.14.8 python-pyfaidx@0.7.2.1 python-pysam@0.23.0 python-reportlab@4.0.8 python-scikit-learn@1.7.0 python-scipy@1.12.0 r-dnacopy@1.84.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://cnvkit.readthedocs.org/
Licenses: ASL 2.0
Build system: pyproject
Synopsis: Copy number variant detection from targeted DNA sequencing
Description:

CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.

homer 4.11.1
Dependencies: perl@5.36.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://homer.ucsd.edu/homer
Licenses: GPL 3+
Build system: gnu
Synopsis: Motif discovery and next generation sequencing analysis
Description:

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. It is a collection of command line programs written in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding 8-20 bp motifs in large scale genomics data. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.

python-biopython 1.73
Propagated dependencies: python-numpy@1.26.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://biopython.org/
Licenses: non-copyleft
Build system: pyproject
Synopsis: Tools for biological computation in Python
Description:

Biopython is a set of tools for biological computation including parsers for bioinformatics files into Python data structures; interfaces to common bioinformatics programs; a standard sequence class and tools for performing common operations on them; code to perform data classification; code for dealing with alignments; code making it easy to split up parallelizable tasks into separate processes; and more.

r-gtrack 0.1.0-1.a694fa3
Propagated dependencies: r-biocgenerics@0.56.0 r-data-table@1.17.8 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-gutils@0.2.0-2.fc24db6 r-iranges@2.44.0 r-matrix@1.7-4 r-rcolorbrewer@1.1-3 r-rcpp@1.1.0 r-rcurl@1.98-1.17 r-rtracklayer@1.70.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/mskilab/gTrack/
Licenses: GPL 2
Build system: r
Synopsis: Plot tracks of complex genomic data across multiple genomic windows
Description:

This package provides an object for plotting GRanges, RleList, UCSC file formats, and ffTrack objects in multi-track panels.

r-raremetals2 0.1
Propagated dependencies: r-seqminer@9.7 r-mvtnorm@1.3-3 r-mass@7.3-65 r-compquadform@1.4.4 r-getopt@1.20.4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: http://genome.sph.umich.edu/wiki/RareMETALS2
Licenses: GPL 3
Build system: r
Synopsis: Analyze gene-level association tests for binary trait
Description:

The R package rareMETALS2 is an extension of the R package rareMETALS. It was designed to meta-analyze gene-level association tests for binary trait. While rareMETALS offers a near-complete solution for meta-analysis of gene-level tests for quantitative trait, it does not offer the optimal solution for binary trait. The package rareMETALS2 offers improved features for analyzing gene-level association tests in meta-analyses for binary trait.

minimap2 2.28
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://lh3.github.io/minimap2/
Licenses: Expat
Build system: gnu
Synopsis: Pairwise aligner for genomic and spliced nucleotide sequences
Description:

Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Typical use cases include:

  1. mapping PacBio or Oxford Nanopore genomic reads to the human genome;

  2. finding overlaps between long reads with error rate up to ~15%;

  3. splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA reads against a reference genome;

  4. aligning Illumina single- or paired-end reads;

  5. assembly-to-assembly alignment;

  6. full-genome alignment between two closely related species with divergence below ~15%.

bwa-meth 0.2.9
Dependencies: bwa@0.7.18 python-toolshed@0.4.6
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/brentp/bwa-meth
Licenses: Expat
Build system: pyproject
Synopsis: Fast and accurante alignment of BS-Seq reads
Description:

BWA-Meth works for single-end reads and for paired-end reads from the directional protocol (most common). It uses the method employed by methylcoder and Bismark of in silico conversion of all C's to T's in both reference and reads. It recovers the original read (needed to tabulate methylation) by attaching it as a comment which BWA appends as a tag to the read. It performs favorably to existing aligners gauged by number of on and off-target reads for a capture method that targets CpG-rich region.

python-harmonypy 0.0.10
Propagated dependencies: python-numpy@1.26.4 python-pandas@2.2.3 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/slowkow/harmonypy
Licenses: GPL 2
Build system: pyproject
Synopsis: Data integration algorithm
Description:

Harmony is an algorithm for integrating multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.

snap-aligner 2.0.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://snap.cs.berkeley.edu/
Licenses: ASL 2.0
Build system: gnu
Synopsis: Short read DNA sequence aligner
Description:

SNAP is a fast and accurate aligner for short DNA reads. It is optimized for modern read lengths of 100 bases or higher, and takes advantage of these reads to align data quickly through a hash-based indexing scheme.

r-metadeconfoundr 0.3.0-1.90aec02
Propagated dependencies: r-bigmemory@4.6.4 r-detectseparation@0.3 r-doparallel@1.0.17 r-dosnow@1.0.20 r-foreach@1.5.2 r-futile-logger@1.4.3 r-ggplot2@4.0.1 r-lme4@1.1-37 r-lmtest@0.9-40 r-reshape2@1.4.5 r-snow@0.4-4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/TillBirkner/metadeconfoundR
Licenses: GPL 2
Build system: r
Synopsis: Check multiple covariates for potential confounding effects
Description:

This package detects naive associations between omics features and metadata in cross-sectional data-sets using non-parametric tests. In a second step, confounding effects between metadata associated to the same omics feature are detected and labeled using nested post-hoc model comparison tests. The generated output can be graphically summarized using the built-in plotting function.

diamond 2.1.6
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/bbuchfink/diamond
Licenses: GPL 3+
Build system: cmake
Synopsis: Accelerated BLAST compatible local sequence aligner
Description:

DIAMOND is a BLAST-compatible local aligner for mapping protein and translated DNA query sequences against a protein reference database (BLASTP and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short reads at a typical sensitivity of 90-99% relative to BLAST depending on the data and settings.

wfmash 0.21.0
Dependencies: atomic-queue@1.6.5 gsl@2.8 htslib@1.21 libdeflate@1.19 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/waveygang/wfmash
Licenses: Expat
Build system: cmake
Synopsis: Base-accurate DNA sequence aligner
Description:

wfmash is a DNA sequence read mapper based on mash distances and the wavefront alignment algorithm. It is a fork of MashMap that implements base-level alignment via the wflign tiled wavefront global alignment algorithm. It completes MashMap with a high-performance alignment module capable of computing base-level alignments for very large sequences.

java-biojava-alignment 4.2.11
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@4.2.11 java-biojava-phylo@4.2.11 java-forester@0-1.86b07ef
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.

r-ggexpress 0.6.6-1.82f1693
Propagated dependencies: r-cowplot@1.2.0 r-ggplot2@4.0.1 r-ggpubr@0.6.2 r-markdownhelpers@0.2.0-1.793372d r-markdownreports@4.5.9-1.3ba1103 r-rcolorbrewer@1.1-3 r-sessioninfo@1.2.3 r-seurat@5.3.1 r-sm@2.2-6.0 r-stringendo@0.6.0-1.15594b1 r-tidyverse@2.0.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/vertesy/ggExpress
Licenses: GPL 3
Build system: r
Synopsis: This is a fast tool to create, annotate and export plots in R
Description:

This package is a set of R functions for generating precise figures. This tool helps you to create clean markdown reports about what you just discovered with your analysis script.

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Total results: 68655