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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:

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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-riboseqr 1.42.0
Propagated dependencies: r-abind@1.4-8 r-bayseq@2.42.0 r-genomeinfodb@1.44.0 r-genomicranges@1.60.0 r-iranges@2.42.0 r-rsamtools@2.24.0 r-s4vectors@0.46.0 r-seqlogo@1.74.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/riboSeqR/
Licenses: GPL 3
Synopsis: Analysis of sequencing data from ribosome profiling experiments
Description:

This package provides plotting functions, frameshift detection and parsing of genetic sequencing data from ribosome profiling experiments.

r-interactionset 1.36.1
Propagated dependencies: r-biocgenerics@0.54.0 r-genomeinfodb@1.44.0 r-genomicranges@1.60.0 r-iranges@2.42.0 r-matrix@1.7-3 r-rcpp@1.0.14 r-s4vectors@0.46.0 r-summarizedexperiment@1.38.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/InteractionSet
Licenses: GPL 3
Synopsis: Base classes for storing genomic interaction data
Description:

This package provides the GInteractions, InteractionSet and ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.

r-pfamanalyzer 1.8.0
Propagated dependencies: r-dplyr@1.1.4 r-magrittr@2.0.3 r-readr@2.1.5 r-stringr@1.5.1 r-tibble@3.2.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/pfamAnalyzeR
Licenses: Expat
Synopsis: Identification of domain isotypes in pfam data
Description:

This R package enables the user to read pfam predictions into R. Most human protein domains exist as multiple distinct variants termed domain isotypes. This R package enables the identification and classification of such domain isotypes from pfam data.

r-infusion 2.2.0
Propagated dependencies: r-blackbox@1.1.46 r-boot@1.3-31 r-cli@3.6.5 r-foreach@1.5.2 r-geometry@0.5.2 r-matrixstats@1.5.0 r-mvtnorm@1.3-3 r-nloptr@2.2.1 r-numderiv@2016.8-1.1 r-pbapply@1.7-2 r-proxy@0.4-27 r-ranger@0.17.0 r-spamm@4.5.0 r-viridislite@0.4.2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://gitlab.mbb.univ-montp2.fr/francois/Infusion
Licenses: CeCILL
Synopsis: Inference using simulation
Description:

This package implements functions for simulation-based inference. In particular, it implements functions to perform likelihood inference from data summaries whose distributions are simulated. The package implements more advanced methods than the ones first described in: Rousset, Gouy, Almoyna and Courtiol (2017) <doi:10.1111/1755-0998.12627>.

r-metabocoreutils 1.16.1
Propagated dependencies: r-biocparallel@1.42.0 r-mscoreutils@1.20.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/RforMassSpectrometry/MetaboCoreUtils
Licenses: Artistic License 2.0
Synopsis: Core utils for Metabolomics data
Description:

MetaboCoreUtils defines metabolomics-related core functionality provided as low-level functions to allow a data structure-independent usage across various R packages. This includes functions to calculate between ion (adduct) and compound mass-to-charge ratios and masses or functions to work with chemical formulas. The package provides also a set of adduct definitions and information on some commercially available internal standard mixes commonly used in MS experiments.

r-erma 1.24.1
Propagated dependencies: r-annotationdbi@1.70.0 r-biobase@2.68.0 r-biocgenerics@0.54.0 r-biocparallel@1.42.0 r-genomeinfodb@1.44.0 r-genomicfiles@1.44.1 r-genomicranges@1.60.0 r-ggplot2@3.5.2 r-homo-sapiens@1.3.1 r-iranges@2.42.0 r-rtracklayer@1.68.0 r-s4vectors@0.46.0 r-shiny@1.10.0 r-summarizedexperiment@1.38.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/erma
Licenses: Artistic License 2.0
Synopsis: Epigenomic road map adventures
Description:

The epigenomics road map describes locations of epigenetic marks in DNA from a variety of cell types. Of interest are locations of histone modifications, sites of DNA methylation, and regions of accessible chromatin. This package presents a selection of elements of the road map including metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines by Ernst and Kellis.

r-psmatch 1.12.0
Propagated dependencies: r-biocgenerics@0.54.0 r-biocparallel@1.42.0 r-igraph@2.1.4 r-iranges@2.42.0 r-matrix@1.7-3 r-mscoreutils@1.20.0 r-protgenerics@1.40.0 r-qfeatures@1.18.0 r-s4vectors@0.46.0 r-spectra@1.18.2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/RforMassSpectrometry/PSM
Licenses: Artistic License 2.0
Synopsis: Handling and managing peptide spectrum matches
Description:

The PSMatch package helps proteomics practitioners to load, handle and manage peptide spectrum matches. It provides functions to model peptide-protein relations as adjacency matrices and connected components, visualise these as graphs and make informed decision about shared peptide filtering. The package also provides functions to calculate and visualise MS2 fragment ions.

r-glad 2.72.0
Dependencies: gsl@2.8
Propagated dependencies: r-aws@2.5-6
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://bioinfo.curie.fr
Licenses: GPL 2
Synopsis: Gain and loss analysis of DNA
Description:

This package helps with the analysis of array CGH data by detecting of the breakpoints in the genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified.

r-dir-expiry 1.16.0
Propagated dependencies: r-filelock@1.0.3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/dir.expiry
Licenses: GPL 3
Synopsis: Managing expiration for cache directories
Description:

This package implements an expiration system for access to versioned directories. Directories that have not been accessed by a registered function within a certain time frame are deleted. This aims to reduce disk usage by eliminating obsolete caches generated by old versions of packages.

r-bsgenome-mmusculus-ucsc-mm9-masked 1.3.99
Propagated dependencies: r-bsgenome@1.76.0 r-bsgenome-mmusculus-ucsc-mm9@1.4.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/
Licenses: Artistic License 2.0
Synopsis: Full masked genome sequences for Mouse
Description:

This package provides full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.

r-motifbreakr 2.22.0
Propagated dependencies: r-biocfilecache@2.16.0 r-biocgenerics@0.54.0 r-biocparallel@1.42.0 r-biomart@2.64.0 r-biostrings@2.76.0 r-bsgenome@1.76.0 r-bsicons@0.1.2 r-bslib@0.9.0 r-dt@0.33 r-genomeinfodb@1.44.0 r-genomicranges@1.60.0 r-gviz@1.52.0 r-iranges@2.42.0 r-matrixstats@1.5.0 r-motifdb@1.50.0 r-motifstack@1.52.0 r-pwalign@1.4.0 r-rtracklayer@1.68.0 r-s4vectors@0.46.0 r-shiny@1.10.0 r-stringr@1.5.1 r-summarizedexperiment@1.38.1 r-tfmpvalue@0.0.9 r-variantannotation@1.54.1 r-vroom@1.6.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/motifbreakR/
Licenses: GPL 2+
Synopsis: Predicting disruptiveness of single nucleotide polymorphisms
Description:

This package allows biologists to judge in the first place whether the sequence surrounding the polymorphism is a good match, and in the second place how much information is gained or lost in one allele of the polymorphism relative to another. This package gives a choice of algorithms for interrogation of genomes with motifs from public sources:

  1. a weighted-sum probability matrix;

  2. log-probabilities;

  3. weighted by relative entropy.

This package can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. Lastly, it can be used to interrogate any genome curated within Bioconductor.

r-affycompatible 1.58.0
Propagated dependencies: r-biostrings@2.76.0 r-rcurl@1.98-1.17 r-xml@3.99-0.18
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AffyCompatible/
Licenses: Artistic License 2.0
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-aucell 1.30.1
Propagated dependencies: r-biocgenerics@0.54.0 r-data-table@1.17.4 r-delayedarray@0.34.1 r-delayedmatrixstats@1.30.0 r-gseabase@1.70.0 r-matrix@1.7-3 r-mixtools@2.0.0.1 r-r-utils@2.13.0 r-summarizedexperiment@1.38.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AUCell/
Licenses: GPL 3
Synopsis: Analysis of gene set activity in single-cell RNA-seq data
Description:

AUCell identifies cells with active gene sets (e.g. signatures, gene modules, etc) in single-cell RNA-seq data. AUCell uses the Area Under the Curve (AUC) to calculate whether a critical subset of the input gene set is enriched within the expressed genes for each cell. The distribution of AUC scores across all the cells allows exploring the relative expression of the signature. Since the scoring method is ranking-based, AUCell is independent of the gene expression units and the normalization procedure. In addition, since the cells are evaluated individually, it can easily be applied to bigger datasets, subsetting the expression matrix if needed.

r-ebseq 2.6.0
Propagated dependencies: r-bh@1.87.0-1 r-blockmodeling@1.1.5 r-gplots@3.2.0 r-rcpp@1.0.14 r-rcppeigen@0.3.4.0.2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/EBSeq
Licenses: Artistic License 2.0
Synopsis: Differential expression analysis of RNA-seq data
Description:

This package provides tools for differential expression analysis at both gene and isoform level using RNA-seq data

r-enrichedheatmap 1.38.0
Propagated dependencies: r-circlize@0.4.16 r-complexheatmap@2.24.0 r-genomicranges@1.60.0 r-getoptlong@1.0.5 r-iranges@2.42.0 r-locfit@1.5-9.12 r-matrixstats@1.5.0 r-rcpp@1.0.14
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/jokergoo/EnrichedHeatmap
Licenses: Expat
Synopsis: Enriched heatmaps
Description:

Enriched heatmap is a special type of heatmap which visualizes the enrichment of genomic signals on specific target regions. This type of heatmap is just a normal heatmap but with some special settings, with the functionality of ComplexHeatmap, it would be much easier to customize the heatmap as well as concatenating to a list of heatmaps to show correspondence between different data sources.

r-bigmemoryextras 1.38.0
Propagated dependencies: r-bigmemory@4.6.4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/phaverty/bigmemoryExtras
Licenses: Artistic License 2.0
Synopsis: Extension of the bigmemory package
Description:

This package defines a BigMatrix ReferenceClass which adds safety and convenience features to the filebacked.big.matrix class from the bigmemory package. BigMatrix protects against segfaults by monitoring and gracefully restoring the connection to on-disk data and it also protects against accidental data modification with a file-system-based permissions system. Utilities are provided for using BigMatrix-derived classes as assayData matrices within the Biobase package's eSet family of classes. BigMatrix provides some optimizations related to attaching to, and indexing into, file-backed matrices with dimnames. Additionally, the package provides a BigMatrixFactor class, a file-backed matrix with factor properties.

r-ctc 1.82.0
Propagated dependencies: r-amap@0.8-20
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ctc/
Licenses: GPL 2
Synopsis: Cluster and tree conversion
Description:

This package provides tools for exporting and importing classification trees and clusters to other programs.

r-aims 1.40.0
Propagated dependencies: r-biobase@2.68.0 r-e1071@1.7-16
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://git.bioconductor.org/packages/AIMS
Licenses: Artistic License 2.0
Synopsis: Absolute assignment of breast cancer intrinsic molecular subtype
Description:

This package contains an implementation of AIMS -- Absolute Intrinsic Molecular Subtyping. It contains necessary functions to assign the five intrinsic molecular subtypes (Luminal A, Luminal B, Her2-enriched, Basal-like, Normal-like). Assignments could be done on individual samples as well as on dataset of gene expression data.

r-impute 1.82.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/impute
Licenses: GPL 2+
Synopsis: Imputation for microarray data
Description:

This package provides a function to impute missing gene expression microarray data, using nearest neighbor averaging.

r-genomicalignments 1.44.0
Propagated dependencies: r-biocgenerics@0.54.0 r-biocparallel@1.42.0 r-biostrings@2.76.0 r-genomeinfodb@1.44.0 r-genomicranges@1.60.0 r-iranges@2.42.0 r-rsamtools@2.24.0 r-s4vectors@0.46.0 r-summarizedexperiment@1.38.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/GenomicAlignments
Licenses: Artistic License 2.0
Synopsis: Representation and manipulation of short genomic alignments
Description:

This package provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

r-hybridmtest 1.52.0
Propagated dependencies: r-biobase@2.68.0 r-fdrtool@1.2.18 r-mass@7.3-65 r-survival@3.8-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/HybridMTest
Licenses: GPL 2+
Synopsis: Hybrid multiple testing
Description:

This package performs hybrid multiple testing that incorporates method selection and assumption evaluations into the analysis using EBP estimates obtained by Grenander density estimation. For instance, for 3-group comparison analysis, Hybrid Multiple testing considers EBPs as weighted EBPs between F-test and H-test with EBPs from Shapiro Wilk test of normality as weight. Instead of just using EBPs from F-test only or using H-test only, this methodology combines both types of EBPs through EBPs from Shapiro Wilk test of normality. This methodology uses then the law of total EBPs.

r-parody 1.66.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/parody
Licenses: Artistic License 2.0
Synopsis: Parametric and resistant outlier detection
Description:

The parody package provides routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics.

r-aneufinderdata 1.36.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AneuFinderData/
Licenses: Artistic License 2.0
Synopsis: Data package for @code{AneuFinder}
Description:

This package contains whole-genome single cell sequencing data for demonstration purposes in the AneuFinder package.

r-ebimage 4.50.0
Propagated dependencies: r-abind@1.4-8 r-biocgenerics@0.54.0 r-fftwtools@0.9-11 r-htmltools@0.5.8.1 r-htmlwidgets@1.6.4 r-jpeg@0.1-11 r-locfit@1.5-9.12 r-png@0.1-8 r-rcurl@1.98-1.17 r-tiff@0.1-12
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/aoles/EBImage
Licenses: LGPL 2.1+
Synopsis: Image processing and analysis toolbox for R
Description:

EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.

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Total results: 45109