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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.


r-monocle 2.38.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biocviews@1.78.0 r-cluster@2.1.8.1 r-combinat@0.0-8 r-ddrtree@0.1.5 r-dplyr@1.1.4 r-fastica@1.2-7 r-ggplot2@4.0.1 r-hsmmsinglecell@1.30.0 r-igraph@2.2.1 r-irlba@2.3.5.1 r-leidenbase@0.1.35 r-limma@3.66.0 r-mass@7.3-65 r-matrix@1.7-4 r-matrixstats@1.5.0 r-pheatmap@1.0.13 r-plyr@1.8.9 r-proxy@0.4-27 r-rann@2.6.2 r-rcpp@1.1.0 r-reshape2@1.4.5 r-rtsne@0.17 r-slam@0.1-55 r-stringr@1.6.0 r-tibble@3.3.0 r-vgam@1.1-13 r-viridis@0.6.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/monocle
Licenses: Artistic License 2.0
Build system: r
Synopsis: Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq
Description:

Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.

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.

star 2.7.3a
Dependencies: htslib@1.21 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/alexdobin/STAR
Licenses: GPL 3+
Build system: gnu
Synopsis: Universal RNA-seq aligner
Description:

The Spliced Transcripts Alignment to a Reference (STAR) software is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences.

bcftools 1.21
Dependencies: gsl@2.8 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://samtools.github.io/bcftools/
Licenses: GPL 3+ Expat
Build system: gnu
Synopsis: Utilities for variant calling and manipulating VCFs and BCFs
Description:

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

ngless 1.5.0
Dependencies: bash-minimal@5.2.37 prodigal@2.6.3 bwa@0.7.18 samtools@1.19 minimap2@2.28 megahit@1.2.9 ghc-missingh@1.5.0.1 ghc-aeson@2.0.3.0 ghc-ansi-terminal@0.11.4 ghc-async@2.2.4 ghc-atomic-write@0.2.0.7 ghc-bytestring-lexing@0.5.0.10 ghc-conduit@1.3.5 ghc-conduit-algorithms@0.0.13.0 ghc-conduit-extra@1.3.6 ghc-configurator@0.3.0.0 ghc-convertible@1.1.1.1 ghc-data-default@0.7.1.1 ghc-edit-distance@0.2.2.1 ghc-either@5.0.2 ghc-errors@2.3.0 ghc-extra@1.7.13 ghc-file-embed@0.0.15.0 ghc-filemanip@0.3.6.3 ghc-hashable@1.4.2.0 ghc-hashtables@1.3.1 ghc-hostname@1.0 ghc-http-client@0.7.13.1 ghc-http-conduit@2.3.8.1 ghc-inline-c@0.9.1.8 ghc-inline-c-cpp@0.5.0.0 ghc-int-interval-map@0.0.0.0 ghc-network@3.1.4.0 ghc-optparse-applicative@0.17.1.0 ghc-primitive@0.7.3.0 ghc-random-shuffle@0.0.4 ghc-regex@1.1.0.2 ghc-resourcet@1.2.6 ghc-safe@0.3.19 ghc-stm-chans@3.0.0.9 ghc-stm-conduit@4.0.1 ghc-strict@0.4.0.1 ghc-tar@0.5.1.1 ghc-tar-conduit@0.3.2 ghc-unix-compat@0.5.4 ghc-unliftio@0.2.25.0 ghc-unliftio-core@0.2.1.0 ghc-vector@0.12.3.1 ghc-vector-algorithms@0.8.0.4 ghc-yaml@0.11.11.1 ghc-zlib@0.6.3.0 ghc-bzlib-conduit@0.3.0.2 ghc-double-conversion@2.0.4.2 ghc-safeio@0.0.5.0
Propagated dependencies: r-r6@2.6.1 r-hdf5r@1.3.12 r-iterators@1.0.14 r-itertools@0.1-3 r-matrix@1.7-4
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://ngless.embl.de/
Licenses: Expat
Build system: haskell
Synopsis: DSL for processing next-generation sequencing data
Description:

Ngless is a domain-specific language for next-generation sequencing (NGS) data processing.

nanosv 1.2.4
Dependencies: python-configparser@7.2.0 python-pysam@0.23.0 python-pyvcf3@1.0.3-0.1fb3789
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/mroosmalen/nanosv
Licenses: Expat
Build system: pyproject
Synopsis: Structural variation detection tool for Oxford Nanopore data
Description:

NanoSV is a software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies’ MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers.

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.

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-cytonorm 0.0.10-1.166f9ff
Propagated dependencies: r-cytoml@2.22.0 r-dplyr@1.1.4 r-emdist@0.3-3 r-flowcore@2.22.0 r-flowsom@2.18.0 r-flowworkspace@4.22.0 r-ggplot2@4.0.1 r-gridextra@2.3 r-pheatmap@1.0.13 r-stringr@1.6.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/saeyslab/CytoNorm
Licenses: GPL 2+
Build system: r
Synopsis: Normalize cytometry data measured across multiple batches
Description:

This package can be used to normalize cytometry samples when a control sample is taken along in each of the batches. This is done by first identifying multiple clusters/cell types, learning the batch effects from the control samples and applying quantile normalization on all markers of interest.

libgff 2.0.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/COMBINE-lab/libgff
Licenses: X11-style
Build system: cmake
Synopsis: Parser library for reading/writing GFF files
Description:

This is a simple "libraryfication" of the GFF/GTF parsing code that is used in the Cufflinks codebase. The goal of this library is to provide this functionality without the necessity of drawing in a heavy-weight dependency like SeqAn.

r-markdownhelpers 0.2.0-1.793372d
Propagated dependencies: r-devtools@2.4.6 r-stringendo@0.6.0-1.15594b1 r-usethis@3.2.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/vertesy/MarkdownHelpers
Licenses: GPL 3
Build system: r
Synopsis: Helper functions for MarkdownReports and ggExpress
Description:

This package provides a set of R functions to parse markdown and other generic helpers.

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.

fastqc 0.11.9
Dependencies: icedtea@3.19.0 java-cisd-jhdf5@14.12.6-39162 java-picard@1.113 java-jbzip2@0.9.1 perl@5.36.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Licenses: GPL 3+
Build system: ant
Synopsis: Quality control tool for high throughput sequence data
Description:

FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.

The main functions of FastQC are:

  • Import of data from BAM, SAM or FastQ files (any variant);

  • Providing a quick overview to tell you in which areas there may be problems;

  • Summary graphs and tables to quickly assess your data;

  • Export of results to an HTML based permanent report;

  • Offline operation to allow automated generation of reports without running the interactive application.

pigx-rnaseq 0.1.1
Dependencies: coreutils@9.1 sed@4.9 gzip@1.14 snakemake@7.32.4 megadepth@1.1.1 multiqc@1.14 star@2.7.3a hisat2@2.2.1 fastp@0.23.2 htseq@2.0.2 samtools@1.19 r-minimal@4.5.2 r-rmarkdown@2.30 r-genomeinfodb@1.46.0 r-ggplot2@4.0.1 r-ggpubr@0.6.2 r-ggrepel@0.9.6 r-gprofiler2@0.2.4 r-deseq2@1.50.2 r-dt@0.34.0 r-knitr@1.50 r-pheatmap@1.0.13 r-corrplot@0.95 r-reshape2@1.4.5 r-plotly@4.11.0 r-scales@1.4.0 r-summarizedexperiment@1.40.0 r-crosstalk@1.2.2 r-tximport@1.38.1 r-rtracklayer@1.70.0 r-rjson@0.2.23 salmon@1.10.3 pandoc@2.19.2 python-wrapper@3.11.14 python-deeptools@3.5.5 python-pyyaml@6.0.2
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://bioinformatics.mdc-berlin.de/pigx/
Licenses: GPL 3+
Build system: gnu
Synopsis: Analysis pipeline for RNA sequencing experiments
Description:

PiGX RNAseq is an analysis pipeline for preprocessing and reporting for RNA sequencing experiments. It is easy to use and produces high quality reports. The inputs are reads files from the sequencing experiment, and a configuration file which describes the experiment. In addition to quality control of the experiment, the pipeline produces a differential expression report comparing samples in an easily configurable manner.

intervaltree 0.0.0-1.b90527f
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/ekg/intervaltree
Licenses: Expat
Build system: gnu
Synopsis: Minimal C++ interval tree implementation
Description:

An interval tree can be used to efficiently find a set of numeric intervals overlapping or containing another interval. This library provides a basic implementation of an interval tree using C++ templates, allowing the insertion of arbitrary types into the tree.

mafft 7.475
Dependencies: bash-minimal@5.2.37 perl@5.36.0 ruby@3.3.9 gawk@5.3.0 grep@3.11 coreutils@9.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://mafft.cbrc.jp/alignment/software/
Licenses: non-copyleft
Build system: gnu
Synopsis: Multiple sequence alignment program
Description:

MAFFT offers a range of multiple alignment methods for nucleotide and protein sequences. For instance, it offers L-INS-i (accurate; for alignment of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000 sequences).

python-modbedtools 0.1.6
Propagated dependencies: python-pysam@0.23.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/lidaof/modbedtools
Licenses: Expat
Build system: pyproject
Synopsis: Generate modbed track files for visualization on WashU Epigenome Browser
Description:

modbedtools is a python command line tool to generate modbed files for visualization on the WashU Epigenome Browser.

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.

segemehl 0.3.4
Dependencies: htslib@1.21 ncurses@6.2.20210619 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://www.bioinf.uni-leipzig.de/Software/segemehl
Licenses: GPL 3+
Build system: gnu
Synopsis: Map short sequencer reads to reference genomes
Description:

Segemehl is software to map short sequencer reads to reference genomes. Segemehl implements a matching strategy based on enhanced suffix arrays (ESA). It accepts fasta and fastq queries (gzip'ed and bgzip'ed). In addition to the alignment of reads from standard DNA- and RNA-seq protocols, it also allows the mapping of bisulfite converted reads (Lister and Cokus) and implements a split read mapping strategy. The output of segemehl is a SAM or BAM formatted alignment file.

pairadise 1.0.0
Dependencies: star@2.7.8a
Propagated dependencies: python-pysam@0.23.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/Xinglab/PAIRADISE
Licenses: GPL 3+
Build system: pyproject
Synopsis: Paired replicate analysis of allelic differential splicing events
Description:

PAIRADISE is a method for detecting allele-specific alternative splicing (ASAS) from RNA-seq data. Unlike conventional approaches that detect ASAS events one sample at a time, PAIRADISE aggregates ASAS signals across multiple individuals in a population. By treating the two alleles of an individual as paired, and multiple individuals sharing a heterozygous SNP as replicates, PAIRADISE formulates ASAS detection as a statistical problem for identifying differential alternative splicing from RNA-seq data with paired replicates.

samtools 1.19
Dependencies: htslib@1.21 ncurses@6.2.20210619 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://samtools.sourceforge.net
Licenses: Expat
Build system: gnu
Synopsis: Utilities to efficiently manipulate nucleotide sequence alignments
Description:

Samtools implements various utilities for post-processing nucleotide sequence alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer.

r-copykat 1.0.8-0.256de33
Propagated dependencies: r-cluster@2.1.8.1 r-dlm@1.1-6.1 r-gplots@3.2.0 r-mcmcpack@1.7-1 r-mixtools@2.0.0.1 r-paralleldist@0.2.7 r-rcolorbrewer@1.1-3
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/navinlabcode/copykat
Licenses: GPL 2
Build system: r
Synopsis: Inference of genomic copy number from single cell RNAseq data
Description:

This package Copynumber KAryotyping of Tumors infers genomic copy number and subclonal structure of human tumors using integrative Bayesian approaches to identify genome-wide aneuploidy at 5MB resolution in single cells data. It separates tumor cells and tumor subclones from normal cells using high-throughput sc-RNAseq data.

r-skitools 0.0.0.9000-2.ba322dc
Propagated dependencies: r-biostrings@2.78.0 r-complexheatmap@2.26.0 r-data-table@1.17.8 r-devtools@2.4.6 r-dt@0.34.0 r-gchain@0.2.0-2.19f8bb9 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-gplots@3.2.0 r-gutils@0.2.0-2.fc24db6 r-htmlwidgets@1.6.4 r-hwriter@1.3.2.1 r-igraph@2.2.1 r-iranges@2.44.0 r-plotly@4.11.0 r-rcolorbrewer@1.1-3 r-reshape2@1.4.5 r-s4vectors@0.48.0 r-stringr@1.6.0 r-variantannotation@1.56.0
Channel: guix
Location: gnu/packages/bioinformatics.scm (gnu packages bioinformatics)
Home page: https://github.com/mskilab/skitools/
Licenses: Expat
Build system: r
Synopsis: Various mskilab R utilities
Description:

This package provides R miscellaneous utilities for basic data manipulation, debugging, visualization, lsf management, and common mskilab tasks.

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.

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