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      /\__ \     / /\ \ \\ \ \_/ / /     / / /\ \__
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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.

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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-parathyroidse 1.46.0
Propagated dependencies: r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/parathyroidSE
Licenses: LGPL 2.1+
Build system: r
Synopsis: RangedSummarizedExperiment for RNA-Seq of parathyroid tumors
Description:

This package provides RangedSummarizedExperiment objects of read counts in genes and exonic parts for paired-end RNA-Seq data from experiments on primary cultures of parathyroid tumors. The sequencing was performed on tumor cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and control).

r-amountain 1.36.0
Dependencies: gsl@2.8
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AMOUNTAIN
Licenses: GPL 2+
Build system: r
Synopsis: Modules for multilayer weighted gene co-expression networks
Description:

This package provides a pure data-driven gene network, WGCN(weighted gene co-expression network) could be constructed only from expression profile. Different layers in such networks may represent different time points, multiple conditions or various species. AMOUNTAIN aims to search active modules in multi-layer WGCN using a continuous optimization approach.

r-acgh 1.88.0
Propagated dependencies: r-biobase@2.70.0 r-cluster@2.1.8.1 r-multtest@2.66.0 r-survival@3.8-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/aCGH
Licenses: GPL 2
Build system: r
Synopsis: Classes and functions for array comparative genomic hybridization data
Description:

This package provides functions for reading array comparative genomic hybridization (aCGH) data from image analysis output files and clone information files, creation of aCGH objects for storing these data. Basic methods are accessing/replacing, subsetting, printing and plotting aCGH objects.

r-biscuiteerdata 1.24.0
Propagated dependencies: r-annotationhub@4.0.0 r-curl@7.0.0 r-experimenthub@3.0.0 r-genomicranges@1.62.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/biscuiteerData
Licenses: GPL 3
Build system: r
Synopsis: Data package for Biscuiteer
Description:

This package contains default datasets used by the Bioconductor package biscuiteer.

r-enmix 1.46.0
Propagated dependencies: r-annotationhub@4.0.0 r-biobase@2.70.0 r-doparallel@1.0.17 r-dynamictreecut@1.63-1 r-experimenthub@3.0.0 r-foreach@1.5.2 r-genefilter@1.92.0 r-geneplotter@1.88.0 r-gplots@3.2.0 r-gtools@3.9.5 r-illuminaio@0.52.0 r-impute@1.84.0 r-iranges@2.44.0 r-irlba@2.3.5.1 r-matrixstats@1.5.0 r-minfi@1.56.0 r-quadprog@1.5-8 r-rpmm@1.25 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/release/bioc/html/ENmix.html
Licenses: Artistic License 2.0
Build system: r
Synopsis: Quality control and analysis tools for Illumina DNA methylation BeadChip
Description:

This package provides tools for quality control, analysis and visualization of Illumina DNA methylation array data.

r-motifbreakr 2.24.0
Propagated dependencies: r-biocfilecache@3.0.0 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-biomart@2.66.0 r-biostrings@2.78.0 r-bsgenome@1.78.0 r-bsicons@0.1.2 r-bslib@0.9.0 r-dt@0.34.0 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-gviz@1.54.0 r-iranges@2.44.0 r-matrixstats@1.5.0 r-motifdb@1.52.0 r-motifstack@1.54.0 r-pwalign@1.6.0 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-shiny@1.11.1 r-stringr@1.6.0 r-summarizedexperiment@1.40.0 r-tfmpvalue@0.0.9 r-variantannotation@1.56.0 r-vroom@1.6.6
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/motifbreakR/
Licenses: GPL 2+
Build system: r
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-txdb-mmusculus-ucsc-mm10-ensgene 3.4.0
Propagated dependencies: r-annotationdbi@1.72.0 r-genomicfeatures@1.62.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.ensGene
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation package for TxDb object(s)
Description:

This package exposes an annotation databases generated from UCSC by exposing these as TxDb objects.

r-metabocoreutils 1.18.1
Propagated dependencies: r-biocparallel@1.44.0 r-mscoreutils@1.21.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/RforMassSpectrometry/MetaboCoreUtils
Licenses: Artistic License 2.0
Build system: r
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-ggbio 1.58.0
Propagated dependencies: r-annotationdbi@1.72.0 r-annotationfilter@1.34.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-biovizbase@1.58.0 r-bsgenome@1.78.0 r-ensembldb@2.34.0 r-genomeinfodb@1.46.0 r-genomicalignments@1.46.0 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-gridextra@2.3 r-gtable@0.3.6 r-hmisc@5.2-4 r-iranges@2.44.0 r-organismdbi@1.52.0 r-reshape2@1.4.5 r-rlang@1.1.6 r-rsamtools@2.26.0 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-scales@1.4.0 r-seqinfo@1.0.0 r-summarizedexperiment@1.40.0 r-variantannotation@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://www.tengfei.name/ggbio/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Visualization tools for genomic data
Description:

The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.

r-qdnaseq 1.46.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-cghbase@1.70.0 r-cghcall@2.72.0 r-dnacopy@1.84.0 r-future-apply@1.20.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-matrixstats@1.5.0 r-r-utils@2.13.0 r-rsamtools@2.26.0 r-seqinfo@1.0.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/QDNAseq
Licenses: GPL 2+
Build system: r
Synopsis: Quantitative DNA sequencing for chromosomal aberrations
Description:

The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.

r-human370v1ccrlmm 1.0.2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/human370v1cCrlmm
Licenses: Artistic License 2.0
Build system: r
Synopsis: Metadata for fast genotyping with the 'crlmm' package
Description:

This is a package with metadata for genotyping Illumina 370k arrays using the crlmm package.

r-jaspar2020 0.99.10
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://jaspar.elixir.no/
Licenses: GPL 2
Build system: r
Synopsis: Data package for JASPAR database (version 2020)
Description:

Data package for JASPAR2020. To explore these databases, utilize the TFBSTools package (version 1.23.1 or higher).

r-biomvcclass 1.78.0
Propagated dependencies: r-biobase@2.70.0 r-graph@1.88.0 r-mvcclass@1.84.0 r-rgraphviz@2.54.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BioMVCClass
Licenses: LGPL 2.1+
Build system: r
Synopsis: Model-View-Controller (MVC) classes that use Biobase
Description:

This package contains classes used in model-view-controller (MVC) design.

r-degreport 1.46.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-broom@1.0.10 r-circlize@0.4.16 r-cluster@2.1.8.1 r-complexheatmap@2.26.0 r-consensusclusterplus@1.74.0 r-cowplot@1.2.0 r-dendextend@1.19.1 r-deseq2@1.50.2 r-dplyr@1.1.4 r-edger@4.8.0 r-ggdendro@0.2.0 r-ggplot2@4.0.1 r-ggrepel@0.9.6 r-knitr@1.50 r-logging@0.10-108 r-magrittr@2.0.4 r-psych@2.5.6 r-rcolorbrewer@1.1-3 r-reshape@0.8.10 r-rlang@1.1.6 r-s4vectors@0.48.0 r-scales@1.4.0 r-stringi@1.8.7 r-stringr@1.6.0 r-summarizedexperiment@1.40.0 r-tibble@3.3.0 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://lpantano.github.io/DEGreport/
Licenses: Expat
Build system: r
Synopsis: Report of DEG analysis
Description:

This is a package for creating na HTML report of differential expression analyses of count data. It integrates some of the code mentioned in DESeq2 and edgeR vignettes, and report a ranked list of genes according to the fold changes mean and variability for each selected gene.

r-alabaster-ranges 1.10.0
Propagated dependencies: r-alabaster-base@1.10.0 r-biocgenerics@0.56.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-rhdf5@2.54.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/alabaster.ranges
Licenses: Expat
Build system: r
Synopsis: Load and save Ranges-related artifacts from file
Description:

This is a package for saving GenomicRanges, IRanges and related data structures into file artifacts, and loading them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

r-mafh5-gnomad-v3-1-2-grch38 3.15.1
Propagated dependencies: r-bsgenome@1.78.0 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-genomicscores@2.22.0 r-hdf5array@1.38.0 r-iranges@2.44.0 r-rhdf5@2.54.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/MafH5.gnomAD.v3.1.2.GRCh38
Licenses: Artistic License 2.0
Build system: r
Synopsis: Minor allele frequency data from gnomAD version 3.1.2 for GRCh38
Description:

This package is designed to store minor allele frequency data. It retrieves this data from the Genome Aggregation Database (gnomAD version 3.1.2) for the human genome version GRCh38.

r-classdiscovery 3.4.9
Propagated dependencies: r-biobase@2.70.0 r-cluster@2.1.8.1 r-mclust@6.1.2 r-oompabase@3.2.10 r-oompadata@3.1.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://oompa.r-forge.r-project.org/
Licenses: ASL 2.0
Build system: r
Synopsis: Classes and methods for "Class Discovery" with Microarrays or Proteomics
Description:

This package defines classes for "class discovery" in the OOMPA project. Class discovery primarily consists of unsupervised clustering methods with attempts to assess their statistical significance.

r-bambu 3.12.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-bsgenome@1.78.0 r-data-table@1.17.8 r-dplyr@1.1.4 r-genomeinfodb@1.46.0 r-genomicalignments@1.46.0 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-rcpp@1.1.0 r-rcpparmadillo@15.2.2-1 r-rsamtools@2.26.0 r-s4vectors@0.48.0 r-summarizedexperiment@1.40.0 r-tidyr@1.3.1 r-xgboost@1.7.11.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/GoekeLab/bambu
Licenses: GPL 3
Build system: r
Synopsis: Isoform reconstruction and quantification for long read RNA-Seq data
Description:

This R package is for multi-sample transcript discovery and quantification using long read RNA-Seq data. You can use bambu after read alignment to obtain expression estimates for known and novel transcripts and genes. The output from bambu can directly be used for visualisation and downstream analysis, such as differential gene expression or transcript usage.

r-rtcgatoolbox 2.40.0
Propagated dependencies: r-biocgenerics@0.56.0 r-data-table@1.17.8 r-delayedarray@0.36.0 r-genomicranges@1.62.0 r-httr@1.4.7 r-raggedexperiment@1.34.0 r-rcurl@1.98-1.17 r-rjsonio@2.0.0 r-rvest@1.0.5 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-stringr@1.6.0 r-summarizedexperiment@1.40.0 r-tcgautils@1.30.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://mksamur.github.io/RTCGAToolbox/
Licenses: GPL 2
Build system: r
Synopsis: Export TCGA Firehose data
Description:

Managing data from large scale projects such as The Cancer Genome Atlas (TCGA) for further analysis is an important and time consuming step for research projects. Several efforts, such as Firehose project, make TCGA pre-processed data publicly available via web services and data portals but it requires managing, downloading and preparing the data for following steps. This package provides an extensible R based data client for Firehose pre-processed data.

r-asics 2.26.0
Propagated dependencies: r-biocparallel@1.44.0 r-ggplot2@4.0.1 r-glmnet@4.1-10 r-gridextra@2.3 r-matrix@1.7-4 r-mvtnorm@1.3-3 r-pepsnmr@1.28.0 r-plyr@1.8.9 r-quadprog@1.5-8 r-ropls@1.42.0 r-summarizedexperiment@1.40.0 r-zoo@1.8-14
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ASICS
Licenses: GPL 2+
Build system: r
Synopsis: Automatic statistical identification in complex spectra
Description:

ASICS quantifies concentration of metabolites in a complex spectrum. The identification of metabolites is performed by fitting a mixture model to the spectra of the library with a sparse penalty.

r-survcomp 1.60.0
Propagated dependencies: r-bootstrap@2019.6 r-ipred@0.9-15 r-kernsmooth@2.23-26 r-prodlim@2025.04.28 r-rmeta@3.0 r-suppdists@1.1-9.9 r-survival@3.8-3 r-survivalroc@1.0.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.pmgenomics.ca/bhklab/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Performance assessment and comparison for survival analysis
Description:

This is a package for the assessment and comparison of the performance of risk prediction (survival) models.

r-lfa 2.10.0
Propagated dependencies: r-corpcor@1.6.10 r-rspectra@0.16-2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/StoreyLab/lfa
Licenses: GPL 3
Build system: r
Synopsis: Logistic Factor Analysis for categorical data
Description:

Logistic Factor Analysis (LFA) is a method for a PCA analogue on Binomial data via estimation of latent structure in the natural parameter.

r-structstrings 1.26.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-crayon@1.5.3 r-iranges@2.44.0 r-s4vectors@0.48.0 r-stringi@1.8.7 r-stringr@1.6.0 r-xvector@0.50.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/FelixErnst/Structstrings
Licenses: Artistic License 2.0
Build system: r
Synopsis: Implementation of the dot bracket annotations with Biostrings
Description:

The Structstrings package implements the widely used dot bracket annotation for storing base pairing information in structured RNA. Structstrings uses the infrastructure provided by the Biostrings package and derives the DotBracketString and related classes from the BString class. From these, base pair tables can be produced for in depth analysis. In addition, the loop indices of the base pairs can be retrieved as well. For better efficiency, information conversion is implemented in C, inspired to a large extend by the ViennaRNA package.

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