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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.

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r-mdqc 1.72.0
Propagated dependencies: r-cluster@2.1.8.1 r-mass@7.3-65
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/mdqc
Licenses: LGPL 2.0+
Build system: r
Synopsis: Mahalanobis distance quality control for microarrays
Description:

MDQC is a multivariate quality assessment method for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array's quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality.

r-abaenrichment 1.24.0
Propagated dependencies: r-abadata@1.12.0 r-data-table@1.17.8 r-gofuncr@1.30.0 r-gplots@3.2.0 r-gtools@3.9.5 r-rcpp@1.1.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ABAEnrichment/
Licenses: GPL 2+
Build system: r
Synopsis: Gene expression enrichment in human brain regions
Description:

The package ABAEnrichment is designed to test for enrichment of user defined candidate genes in the set of expressed genes in different human brain regions. The core function aba_enrich integrates the expression of the candidate gene set (averaged across donors) and the structural information of the brain using an ontology, both provided by the Allen Brain Atlas project.

r-oligoclasses 1.72.0
Propagated dependencies: r-affyio@1.80.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biocmanager@1.30.27 r-biostrings@2.78.0 r-dbi@1.2.3 r-ff@4.5.2 r-foreach@1.5.2 r-genomicranges@1.62.0 r-iranges@2.44.0 r-rsqlite@2.4.4 r-s4vectors@0.48.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/oligoClasses/
Licenses: GPL 2+
Build system: r
Synopsis: Classes for high-throughput arrays
Description:

This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages.

r-xllim 2.3
Propagated dependencies: r-abind@1.4-8 r-capushe@1.1.3 r-corpcor@1.6.10 r-e1071@1.7-16 r-glmnet@4.1-10 r-igraph@2.2.1 r-mass@7.3-65 r-matrix@1.7-4 r-mda@0.5-5 r-mixomics@6.34.0 r-progress@1.2.3 r-randomforest@4.7-1.2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://cran.r-project.org/package=xLLiM
Licenses: GPL 2+
Build system: r
Synopsis: High dimensional locally-linear mapping
Description:

This package provides a tool for non linear mapping (non linear regression) using a mixture of regression model and an inverse regression strategy. The methods include the GLLiM model (see Deleforge et al (2015) <DOI:10.1007/s11222-014-9461-5>) based on Gaussian mixtures and a robust version of GLLiM, named SLLiM (see Perthame et al (2016) <DOI:10.1016/j.jmva.2017.09.009>) based on a mixture of Generalized Student distributions. The methods also include BLLiM (see Devijver et al (2017) <arXiv:1701.07899>) which is an extension of GLLiM with a sparse block diagonal structure for large covariance matrices (particularly interesting for transcriptomic data).

r-yarn 1.36.0
Propagated dependencies: r-biobase@2.70.0 r-biomart@2.66.0 r-downloader@0.4.1 r-edger@4.8.0 r-gplots@3.2.0 r-limma@3.66.0 r-matrixstats@1.5.0 r-preprocesscore@1.72.0 r-quantro@1.44.0 r-rcolorbrewer@1.1-3 r-readr@2.1.6
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/yarn/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Robust multi-condition RNA-Seq preprocessing and normalization
Description:

Expedite large RNA-Seq analyses using a combination of previously developed tools. YARN is meant to make it easier for the user in performing basic mis-annotation quality control, filtering, and condition-aware normalization. YARN leverages many Bioconductor tools and statistical techniques to account for the large heterogeneity and sparsity found in very large RNA-seq experiments.

r-ideoviz 1.46.0
Propagated dependencies: r-biobase@2.70.0 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-rcolorbrewer@1.1-3 r-rtracklayer@1.70.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/IdeoViz/
Licenses: GPL 2
Build system: r
Synopsis: Plots data along a chromosomal ideogram
Description:

This package provides functions to plot data associated with arbitrary genomic intervals along chromosomal ideogram.

r-chipexoqualexample 1.34.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.github.com/keleslab/ChIPexoQualExample
Licenses: GPL 2+
Build system: r
Synopsis: Example data for the ChIPexoQual package
Description:

This package contains data for the ChIPexoQual package, consisting of 3 chromosome 1 aligned reads from a ChIP-exo experiment for FoxA1 in mouse liver cell lines aligned to the mm9 genome.

r-rnbeads-hg19 1.42.0
Propagated dependencies: r-genomicranges@1.62.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/RnBeads.hg19
Licenses: GPL 3
Build system: r
Synopsis: RnBeads annotation package for hg19 assembly
Description:

This package is an automatically generated RnBeads annotation package for the assembly hg19.

r-mscoreutils 1.21.0
Propagated dependencies: r-clue@0.3-66 r-mass@7.3-65 r-rcpp@1.1.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/RforMassSpectrometry/MsCoreUtils
Licenses: Artistic License 2.0
Build system: r
Synopsis: Core utils for mass spectrometry data
Description:

This package defines low-level functions for mass spectrometry data and is independent of any high-level data structures. These functions include mass spectra processing functions (noise estimation, smoothing, binning), quantitative aggregation functions (median polish, robust summarisation, etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as well as misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages.

r-timeseriesexperiment 1.13.0
Propagated dependencies: r-deseq2@1.50.2 r-dplyr@1.1.4 r-dynamictreecut@1.63-1 r-edger@4.8.0 r-ggplot2@4.0.1 r-hmisc@5.2-4 r-limma@3.66.0 r-magrittr@2.0.4 r-proxy@0.4-27 r-s4vectors@0.48.0 r-summarizedexperiment@1.40.0 r-tibble@3.3.0 r-tidyr@1.3.1 r-vegan@2.7-2 r-viridis@0.6.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/nlhuong/TimeSeriesExperiment/
Licenses: LGPL 3+
Build system: r
Synopsis: Analysis for short time-series data
Description:

This package is a visualization and analysis toolbox for short time course data which includes dimensionality reduction, clustering, two-sample differential expression testing and gene ranking techniques. The package also provides methods for retrieving enriched pathways.

r-illuminahumanmethylationepicanno-ilm10b2-hg19 0.6.0
Propagated dependencies: r-minfi@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bitbucket.com/kasperdanielhansen/Illumina_EPIC
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation for Illumina's EPIC methylation arrays
Description:

This is an annotation package for Illumina's EPIC methylation arrays.

r-ldblock 1.40.0
Propagated dependencies: r-biocgenerics@0.56.0 r-httr@1.4.7 r-matrix@1.7-4 r-rlang@1.1.6 r-seqinfo@1.0.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ldblock
Licenses: Artistic License 2.0
Build system: r
Synopsis: Data structures for linkage disequilibrium measures in populations
Description:

This package defines data structures for linkage disequilibrium (LD) measures in populations. Its purpose is to simplify handling of existing population-level data for the purpose of flexibly defining LD blocks.

r-tfbstools 1.48.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-biostrings@2.78.0 r-bsgenome@1.78.0 r-catools@1.18.3 r-dbi@1.2.3 r-dirichletmultinomial@1.52.0 r-genomicranges@1.62.0 r-gtools@3.9.5 r-iranges@2.44.0 r-pwalign@1.6.0 r-rsqlite@2.4.4 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-seqlogo@1.76.0 r-tfmpvalue@0.0.9 r-xml@3.99-0.20 r-xvector@0.50.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/ge11232002/TFBSTools
Licenses: GPL 2
Build system: r
Synopsis: Transcription factor binding site (TFBS) analysis
Description:

TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matrix (PFM), Position Weight Matrix (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.

r-genefilter 1.92.0
Propagated dependencies: r-annotate@1.88.0 r-annotationdbi@1.72.0 r-biobase@2.70.0 r-matrixgenerics@1.22.0 r-survival@3.8-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/genefilter
Licenses: Artistic License 2.0
Build system: r
Synopsis: Filter genes from high-throughput experiments
Description:

This package provides basic functions for filtering genes from high-throughput sequencing experiments.

r-goseq 1.62.0
Propagated dependencies: r-annotationdbi@1.72.0 r-biasedurn@2.0.12 r-biocgenerics@0.56.0 r-genelendatabase@1.46.0 r-genomicfeatures@1.62.0 r-go-db@3.22.0 r-mgcv@1.9-4 r-rtracklayer@1.70.0 r-seqinfo@1.0.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/goseq/
Licenses: LGPL 2.0+
Build system: r
Synopsis: Gene Ontology analyser for RNA-seq and other length biased data
Description:

This package provides tools to detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.

r-annotationforge 1.52.0
Propagated dependencies: r-annotationdbi@1.72.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-dbi@1.2.3 r-rcurl@1.98-1.17 r-rsqlite@2.4.4 r-s4vectors@0.48.0 r-xml@3.99-0.20
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AnnotationForge
Licenses: Artistic License 2.0
Build system: r
Synopsis: Code for building annotation database packages
Description:

This package provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi.

r-affycompatible 1.58.0
Propagated dependencies: r-biostrings@2.78.0 r-rcurl@1.98-1.17 r-xml@3.99-0.20
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AffyCompatible/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Work with Affymetrix GeneChip files
Description:

This package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. It also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files.

r-hdo-db 1.0.0
Propagated dependencies: r-annotationdbi@1.72.0 r-dbi@1.2.3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/HDO.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation maps describing the entire Human Disease Ontology
Description:

This package provides a set of annotation maps describing the entire Human Disease Ontology. The annotation data comes from https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology.

r-interactivedisplay 1.48.0
Propagated dependencies: r-annotationdbi@1.72.0 r-biocgenerics@0.56.0 r-biocmanager@1.30.27 r-category@2.76.0 r-ggplot2@4.0.1 r-gridsvg@1.7-7 r-interactivedisplaybase@1.48.0 r-plyr@1.8.9 r-rcolorbrewer@1.1-3 r-reshape2@1.4.5 r-shiny@1.11.1 r-xml@3.99-0.20
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/interactiveDisplay
Licenses: Artistic License 2.0
Build system: r
Synopsis: Package for Shiny web displays of Bioconductor objects
Description:

This package offers interactive Shiny displays for Bioconductor objects. In addition, this package empowers users to develop engaging visualizations and interfaces for working with Bioconductor data.

r-glimma 2.20.0
Propagated dependencies: r-deseq2@1.50.2 r-edger@4.8.0 r-htmlwidgets@1.6.4 r-jsonlite@2.0.0 r-limma@3.66.0 r-s4vectors@0.48.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/Shians/Glimma
Licenses: LGPL 3
Build system: r
Synopsis: Interactive HTML graphics
Description:

This package generates interactive visualisations for analysis of RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an HTML page. The interactions are built on top of the popular static representations of analysis results in order to provide additional information.

r-decontam 1.30.0
Propagated dependencies: r-ggplot2@4.0.1 r-reshape2@1.4.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/benjjneb/decontam
Licenses: Artistic License 2.0
Build system: r
Synopsis: Identification of contaminants in marker-gene and metagenomics data
Description:

This package offers simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. It works on any kind of feature derived from environmental sequencing data (e.g. ASVs, OTUs, taxonomic groups, MAGs, etc). Requires DNA quantitation data or sequenced negative control samples.

r-biosigner 1.38.0
Propagated dependencies: r-biobase@2.70.0 r-e1071@1.7-16 r-multiassayexperiment@1.36.1 r-multidataset@1.38.0 r-randomforest@4.7-1.2 r-ropls@1.42.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/biosigner/
Licenses: CeCILL
Build system: r
Synopsis: Signature discovery from omics data
Description:

Feature selection is critical in omics data analysis to extract restricted and meaningful molecular signatures from complex and high-dimension data, and to build robust classifiers. This package implements a method to assess the relevance of the variables for the prediction performances of the classifier. The approach can be run in parallel with the PLS-DA, Random Forest, and SVM binary classifiers. The signatures and the corresponding 'restricted' models are returned, enabling future predictions on new datasets.

r-graphite 1.56.0
Propagated dependencies: r-annotationdbi@1.72.0 r-dir-expiry@1.18.0 r-graph@1.88.0 r-httr@1.4.7 r-lifecycle@1.0.4 r-purrr@1.2.0 r-rappdirs@0.3.3 r-rlang@1.1.6
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/graphite/
Licenses: AGPL 3+
Build system: r
Synopsis: Networks from pathway databases
Description:

Graphite provides networks derived from eight public pathway databases, and automates the conversion of node identifiers (e.g. from Entrez IDs to gene symbols).

r-agdex 1.58.0
Propagated dependencies: r-biobase@2.70.0 r-gseabase@1.72.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AGDEX
Licenses: GPL 2+
Build system: r
Synopsis: Evaluate agreement of differential expression for cross-species genomics
Description:

The objective of AGDEX is to evaluate whether the results of a pair of two-group differential expression analysis comparisons show a level of agreement that is greater than expected if the group labels for each two-group comparison are randomly assigned. The agreement is evaluated for the entire transcriptome and (optionally) for a collection of pre-defined gene-sets. Additionally, the procedure performs permutation-based differential expression and meta analysis at both gene and gene-set levels of the data from each experiment.

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Total results: 68658