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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-rat2302-db 3.13.0
Propagated dependencies: r-org-rn-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rat2302.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix Rat230_2 Array annotation data (chip rat2302)
Description:

Affymetrix Affymetrix Rat230_2 Array annotation data (chip rat2302) assembled using data from public repositories.

r-rvs 1.32.0
Propagated dependencies: r-snpstats@1.60.0 r-r-utils@2.13.0 r-kinship2@1.9.6.2 r-grain@1.4.5 r-genlib@1.1.10
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RVS
Licenses: GPL 2
Build system: r
Synopsis: Computes estimates of the probability of related individuals sharing a rare variant
Description:

Rare Variant Sharing (RVS) implements tests of association and linkage between rare genetic variant genotypes and a dichotomous phenotype, e.g. a disease status, in family samples. The tests are based on probabilities of rare variant sharing by relatives under the null hypothesis of absence of linkage and association between the rare variants and the phenotype and apply to single variants or multiple variants in a region (e.g. gene-based test).

r-ragene10stprobeset-db 8.8.0
Propagated dependencies: r-org-rn-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/ragene10stprobeset.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix ragene10 annotation data (chip ragene10stprobeset)
Description:

Affymetrix ragene10 annotation data (chip ragene10stprobeset) assembled using data from public repositories.

r-recountmethylation 1.20.0
Propagated dependencies: r-s4vectors@0.48.0 r-rhdf5@2.54.0 r-reticulate@1.44.1 r-rcurl@1.98-1.17 r-r-utils@2.13.0 r-minfi@1.56.0 r-hdf5array@1.38.0 r-delayedmatrixstats@1.32.0 r-biocfilecache@3.0.0 r-basilisk@1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/metamaden/recountmethylation
Licenses: Artistic License 2.0
Build system: r
Synopsis: Access and analyze public DNA methylation array data compilations
Description:

Resources for cross-study analyses of public DNAm array data from NCBI GEO repo, produced using Illumina's Infinium HumanMethylation450K (HM450K) and MethylationEPIC (EPIC) platforms. Provided functions enable download, summary, and filtering of large compilation files. Vignettes detail background about file formats, example analyses, and more. Note the disclaimer on package load and consult the main manuscripts for further info.

r-ragene11stprobeset-db 8.8.0
Propagated dependencies: r-org-rn-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/ragene11stprobeset.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix ragene11 annotation data (chip ragene11stprobeset)
Description:

Affymetrix ragene11 annotation data (chip ragene11stprobeset) assembled using data from public repositories.

r-rmir-hsa 1.0.5
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RmiR.hsa
Licenses: FSDG-compatible
Build system: r
Synopsis: Various databases of microRNA Targets
Description:

Various databases of microRNA Targets.

r-rcyjs 2.32.0
Propagated dependencies: r-httpuv@1.6.16 r-graph@1.88.0 r-browserviz@2.32.0 r-biocgenerics@0.56.0 r-base64enc@0.1-3
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RCyjs
Licenses: Expat
Build system: r
Synopsis: Display and manipulate graphs in cytoscape.js
Description:

Interactive viewing and exploration of graphs, connecting R to Cytoscape.js, using websockets.

r-rgntx 1.11.1
Propagated dependencies: r-txdb-hsapiens-ucsc-hg19-knowngene@3.22.1 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-regioner@1.42.0 r-iranges@2.44.0 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RgnTX
Licenses: Artistic License 2.0
Build system: r
Synopsis: Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity
Description:

RgnTX allows the integration of transcriptome annotations so as to model the complex alternative splicing patterns. It supports the testing of transcriptome elements without clear isoform association, which is often the real scenario due to technical limitations. It involves functions that do permutaion test for evaluating association between features and transcriptome regions.

r-rattus-norvegicus 1.3.1
Propagated dependencies: r-txdb-rnorvegicus-ucsc-rn5-refgene@3.12.0 r-organismdbi@1.52.0 r-org-rn-eg-db@3.22.0 r-go-db@3.22.0 r-genomicfeatures@1.62.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/Rattus.norvegicus
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation package for the Rattus.norvegicus object
Description:

This package contains the Rattus.norvegicus object to access data from several related annotation packages.

r-rarevariantvis 2.38.0
Propagated dependencies: r-variantannotation@1.56.0 r-txdb-hsapiens-ucsc-hg19-knowngene@3.22.1 r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-phastcons100way-ucsc-hg19@3.7.2 r-iranges@2.44.0 r-gtools@3.9.5 r-googlevis@0.7.3 r-genomicscores@2.22.0 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-genomeinfodb@1.46.0 r-bsgenome-hsapiens-ucsc-hg19@1.4.3 r-bsgenome@1.78.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RareVariantVis
Licenses: Artistic License 2.0
Build system: r
Synopsis: suite for analysis of rare genomic variants in whole genome sequencing data
Description:

Second version of RareVariantVis package aims to provide comprehensive information about rare variants for your genome data. It annotates, filters and presents genomic variants (especially rare ones) in a global, per chromosome way. For discovered rare variants CRISPR guide RNAs are designed, so the user can plan further functional studies. Large structural variants, including copy number variants are also supported. Package accepts variants directly from variant caller - for example GATK or Speedseq. Output of package are lists of variants together with adequate visualization. Visualization of variants is performed in two ways - standard that outputs png figures and interactive that uses JavaScript d3 package. Interactive visualization allows to analyze trio/family data, for example in search for causative variants in rare Mendelian diseases, in point-and-click interface. The package includes homozygous region caller and allows to analyse whole human genomes in less than 30 minutes on a desktop computer. RareVariantVis disclosed novel causes of several rare monogenic disorders, including one with non-coding causative variant - keratolythic winter erythema.

r-reactomegsa 1.24.1
Propagated dependencies: r-tidyr@1.3.1 r-summarizedexperiment@1.40.0 r-rcolorbrewer@1.1-3 r-progress@1.2.3 r-jsonlite@2.0.0 r-igraph@2.2.1 r-httr@1.4.7 r-gplots@3.2.0 r-ggplot2@4.0.1 r-dplyr@1.1.4 r-biocsingular@1.26.1 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/reactome/ReactomeGSA
Licenses: Expat
Build system: r
Synopsis: Client for the Reactome Analysis Service for comparative multi-omics gene set analysis
Description:

The ReactomeGSA packages uses Reactome's online analysis service to perform a multi-omics gene set analysis. The main advantage of this package is, that the retrieved results can be visualized using REACTOME's powerful webapplication. Since Reactome's analysis service also uses R to perfrom the actual gene set analysis you will get similar results when using the same packages (such as limma and edgeR) locally. Therefore, if you only require a gene set analysis, different packages are more suited.

r-regsplice 1.36.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-pbapply@1.7-4 r-limma@3.66.0 r-glmnet@4.1-10 r-edger@4.8.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/lmweber/regsplice
Licenses: Expat
Build system: r
Synopsis: L1-regularization based methods for detection of differential splicing
Description:

Statistical methods for detection of differential splicing (differential exon usage) in RNA-seq and exon microarray data, using L1-regularization (lasso) to improve power.

r-rmassbank 3.20.0
Dependencies: openbabel@3.1.1
Propagated dependencies: r-yaml@2.3.10 r-xml@3.99-0.20 r-webchem@1.3.1 r-tidyselect@1.2.1 r-tibble@3.3.0 r-s4vectors@0.48.0 r-rjson@0.2.23 r-readr@2.1.6 r-readjdx@0.6.4 r-rcpp@1.1.0 r-rcdk@3.8.2 r-r-utils@2.13.0 r-purrr@1.2.0 r-mzr@2.44.0 r-msnbase@2.36.0 r-logger@0.4.1 r-httr2@1.2.1 r-httr@1.4.7 r-glue@1.8.0 r-envipat@2.8 r-dplyr@1.1.4 r-digest@0.6.39 r-data-table@1.17.8 r-chemminer@3.62.0 r-biobase@2.70.0 r-assertthat@0.2.1
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RMassBank
Licenses: Artistic License 2.0
Build system: r
Synopsis: Workflow to process tandem MS files and build MassBank records
Description:

Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.

r-rnamodr-ribomethseq 1.24.0
Propagated dependencies: r-s4vectors@0.48.0 r-rnamodr@1.24.0 r-iranges@2.44.0 r-gviz@1.54.0 r-genomicranges@1.62.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/FelixErnst/RNAmodR.RiboMethSeq
Licenses: Artistic License 2.0
Build system: r
Synopsis: Detection of 2'-O methylations by RiboMethSeq
Description:

RNAmodR.RiboMethSeq implements the detection of 2'-O methylations on RNA from experimental data generated with the RiboMethSeq protocol. The package builds on the core functionality of the RNAmodR package to detect specific patterns of the modifications in high throughput sequencing data.

r-rcm 1.26.0
Propagated dependencies: r-vgam@1.1-13 r-tseries@0.10-58 r-tensor@1.5.1 r-reshape2@1.4.5 r-rcolorbrewer@1.1-3 r-phyloseq@1.54.0 r-nleqslv@3.3.5 r-mass@7.3-65 r-ggplot2@4.0.1 r-edger@4.8.0 r-alabama@2023.1.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/release/bioc/vignettes/RCM/inst/doc/RCMvignette.html/
Licenses: GPL 2
Build system: r
Synopsis: Fit row-column association models with the negative binomial distribution for the microbiome
Description:

Combine ideas of log-linear analysis of contingency table, flexible response function estimation and empirical Bayes dispersion estimation for explorative visualization of microbiome datasets. The package includes unconstrained as well as constrained analysis. In addition, diagnostic plot to detect lack of fit are available.

r-rnaeditr 1.20.0
Propagated dependencies: r-survival@3.8-3 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-plyr@1.8.9 r-logistf@1.26.1 r-iranges@2.44.0 r-genomicranges@1.62.0 r-corrplot@0.95 r-bumphunter@1.52.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/TransBioInfoLab/rnaEditr
Licenses: GPL 3
Build system: r
Synopsis: Statistical analysis of RNA editing sites and hyper-editing regions
Description:

RNAeditr analyzes site-specific RNA editing events, as well as hyper-editing regions. The editing frequencies can be tested against binary, continuous or survival outcomes. Multiple covariate variables as well as interaction effects can also be incorporated in the statistical models.

r-remp 1.34.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-settings@0.2.7 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-readr@2.1.6 r-ranger@0.17.0 r-org-hs-eg-db@3.22.0 r-minfi@1.56.0 r-kernlab@0.9-33 r-iterators@1.0.14 r-iranges@2.44.0 r-impute@1.84.0 r-genomicranges@1.62.0 r-foreach@1.5.2 r-doparallel@1.0.17 r-caret@7.0-1 r-bsgenome@1.78.0 r-biostrings@2.78.0 r-biocparallel@1.44.0 r-biocgenerics@0.56.0 r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/YinanZheng/REMP
Licenses: GPL 3
Build system: r
Synopsis: Repetitive Element Methylation Prediction
Description:

Machine learning-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE.

r-rtu34probe 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rtu34probe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type rtu34
Description:

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RT-U34\_probe\_tab.

r-rcpi 1.46.0
Propagated dependencies: r-rlang@1.1.6 r-jsonlite@2.0.0 r-httr2@1.2.1 r-gosemsim@2.36.0 r-foreach@1.5.2 r-doparallel@1.0.17 r-curl@7.0.0 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://nanx.me/Rcpi/
Licenses: Artistic License 2.0 FSDG-compatible
Build system: r
Synopsis: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
Description:

This package provides a molecular informatics toolkit with an integration of bioinformatics and chemoinformatics tools for drug discovery.

r-rgu34acdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rgu34acdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: rgu34acdf
Description:

This package provides a package containing an environment representing the RG_U34A.cdf file.

r-recount3 1.20.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-sessioninfo@1.2.3 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-r-utils@2.13.0 r-matrix@1.7-4 r-httr@1.4.7 r-genomicranges@1.62.0 r-data-table@1.17.8 r-biocfilecache@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/LieberInstitute/recount3
Licenses: Artistic License 2.0
Build system: r
Synopsis: Explore and download data from the recount3 project
Description:

The recount3 package enables access to a large amount of uniformly processed RNA-seq data from human and mouse. You can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level with sample metadata and QC statistics. In addition we provide access to sample coverage BigWig files.

r-rbwa 1.14.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/Jfortin1/Rbwa
Licenses: Expat
Build system: r
Synopsis: R wrapper for BWA-backtrack and BWA-MEM aligners
Description:

This package provides an R wrapper for BWA alignment algorithms. Both BWA-backtrack and BWA-MEM are available. Convenience function to build a BWA index from a reference genome is also provided. Currently not supported for Windows machines.

r-rbm 1.42.0
Propagated dependencies: r-marray@1.88.0 r-limma@3.66.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RBM
Licenses: GPL 2+
Build system: r
Synopsis: RBM: a R package for microarray and RNA-Seq data analysis
Description:

Use A Resampling-Based Empirical Bayes Approach to Assess Differential Expression in Two-Color Microarrays and RNA-Seq data sets.

r-reusedata 1.10.0
Propagated dependencies: r-yaml@2.3.10 r-s4vectors@0.48.0 r-rcwlpipelines@1.26.0 r-rcwl@1.26.0 r-jsonlite@2.0.0 r-biocfilecache@3.0.0 r-basilisk@1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/rworkflow/ReUseData
Licenses: GPL 3
Build system: r
Synopsis: Reusable and reproducible Data Management
Description:

ReUseData is an _R/Bioconductor_ software tool to provide a systematic and versatile approach for standardized and reproducible data management. ReUseData facilitates transformation of shell or other ad hoc scripts for data preprocessing into workflow-based data recipes. Evaluation of data recipes generate curated data files in their generic formats (e.g., VCF, bed). Both recipes and data are cached using database infrastructure for easy data management and reuse. Prebuilt data recipes are available through ReUseData portal ("https://rcwl.org/dataRecipes/") with full annotation and user instructions. Pregenerated data are available through ReUseData cloud bucket that is directly downloadable through "getCloudData()".

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Total results: 68655