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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DT Resource Report Resource Website 1+ mentions |
DT (RRID:SCR_024270) | software toolkit, software resource | Software R package for data objects in R to render as HTML tables using JavaScript library DataTables. DataTables library has been included in this R package. | data objects in R, HTML tables, JavaScript library DataTables, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-dt/ | SCR_024270 | DT: A Wrapper of the JavaScript Library 'DataTables', r-cran-dt, DataTables | 2026-08-05 10:48:01 | 3 | ||||||||
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PiGx-RNAseq Resource Report Resource Website |
PiGx-RNAseq (RRID:SCR_024160) | software toolkit, software resource | Software reproducible genomics analysis pipelines with GNU Guix. Used for analysis of RNA sequencing, chromatin immunoprecipitation sequencing, bisulfite-treated DNA sequencing, and single-cell resolution RNA sequencing. All pipelines process raw experimental data and generate reports containing publication-ready plots and figures, with interactive report elements and standard observables. | reproducible genomics analysis pipelines, GNU Guix, RNA sequencing analysis, chromatin immunoprecipitation sequencing analysis, bisulfite-treated DNA sequencing analysis, single cell resolution RNA sequencing analysis, | is listed by: Debian | PMID:30277498 | Free, Available for download, Freely available, | OMICS_33677 | https://sources.debian.org/src/pigx-rnaseq/ | SCR_024160 | pigx-rnaseq | 2026-08-05 10:47:59 | 0 | ||||||
|
rbgl Resource Report Resource Website |
rbgl (RRID:SCR_024251) | software toolkit, software resource | Software R package as interface to the graph algorithms contained in the BOOST library. | interface to the graph algorithm, BOOST library, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-rbgl/ | SCR_024251 | 2026-08-05 10:48:01 | 0 | |||||||||
|
pcaMethods Resource Report Resource Website 10+ mentions |
pcaMethods (RRID:SCR_024252) | software toolkit, software resource | Software R package providing PCA methods for incomplete data. Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and conventional SVD PCA. Cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. | PCA methods for incomplete data, missing value estimation, | is listed by: Debian | PMID:17344241 | Free, Available for download, Freely available, | OMICS_14344 | https://sources.debian.org/src/r-bioc-pcamethods/ | SCR_024252 | pcamethods | 2026-08-05 10:48:00 | 11 | ||||||
|
rcpi Resource Report Resource Website |
rcpi (RRID:SCR_024253) | software toolkit, software resource | Software R package as molecular informatics toolkit with integration of bioinformatics and chemoinformatics tools for drug discovery. | drug discovery, bioinformatics and chemoinformatics integration, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-rcpi/ | SCR_024253 | 2026-08-05 10:48:00 | 0 | |||||||||
|
rgsepd Resource Report Resource Website |
rgsepd (RRID:SCR_024256) | software toolkit, software resource | Software R package to help disambiguate transcriptome samples by automating differential expression, then gene set enrichment, and finally N-dimensional projection to quantify in which ways each sample is like either treatment group. | disambiguate transcriptome samples, automating differential expression, gene set enrichment, N-dimensional projection, treatment group, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-rgsepd/ | SCR_024256 | 2026-08-05 10:48:01 | 0 | |||||||||
|
makecdfenv Resource Report Resource Website 1+ mentions |
makecdfenv (RRID:SCR_024248) | software toolkit, software resource | Software R package has two functions. One reads Affymetrix chip description file and creates hash table environment containing location/probe set membership mapping. The other creates package that automatically loads that environment. | read Affymetrix chip description file, create hash table environment, location, probe, set membership mapping, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-makecdfenv/ | SCR_024248 | 2026-08-05 10:48:01 | 1 | |||||||||
|
beeswarm Resource Report Resource Website |
beeswarm (RRID:SCR_024262) | software toolkit, software resource | Software R package implementing bee swarm plots. Bee swarm plot is one-dimensional scatter plot like "stripchart", but with closely packed, non overlapping points. | bee swarm plots, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-beeswarm/ | SCR_024262 | an Alternative to Stripchart, r-cran-beeswarm, The Bee Swarm Plot, beeswarm: The Bee Swarm Plot | 2026-08-05 10:48:01 | 0 | ||||||||
|
adephylo Resource Report Resource Website 1+ mentions |
adephylo (RRID:SCR_024267) | software toolkit, software resource | Software R package provides multivariate tools to analyze comparative data. Analysis of comparative evolutionary data. Used for investigating phylogenetic signal in biological traits. | analyze comparative data, investigating phylogenetic signal, biological traits, investigating phylogenetic signal in biological traits, comparative evolutionary data analysis, | is listed by: Debian | PMID:20525823 | Free, Available for download, Freely available, | OMICS_08682 | https://sources.debian.org/src/r-cran-adephylo/ | SCR_024267 | 2026-08-05 10:48:00 | 3 | |||||||
|
tfbstools Resource Report Resource Website 10+ mentions |
tfbstools (RRID:SCR_024260) | software toolkit, software resource | Software R package for analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (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. | analysis and manipulation of transcription factor binding sites, transcription factor binding sites analysis, transcription factor binding sites manipulation, | is listed by: Debian | PMID:26794315 | Free, Available for download, Freely available, | OMICS_11082 | https://sources.debian.org/src/r-bioc-tfbstools/ | SCR_024260 | TFBSTools | 2026-08-05 10:48:02 | 16 | ||||||
|
bsgenome Resource Report Resource Website 10+ mentions |
bsgenome (RRID:SCR_024230) | software toolkit, software resource | Software R package provides infrastructure shared by all the Biostrings-based genome data packages. | infrastructure shared, Biostrings-based genome data packages, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-bsgenome/ | SCR_024230 | 2026-08-05 10:48:01 | 10 | |||||||||
|
ctc Resource Report Resource Website |
ctc (RRID:SCR_024232) | software toolkit, software resource | Software R package for export and import classification trees and clusters to other programs. | export and import classification trees and clusters, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-ctc/ | SCR_024232 | 2026-08-05 10:48:00 | 0 | |||||||||
|
geneplotter Resource Report Resource Website |
geneplotter (RRID:SCR_024234) | software toolkit, software resource | Software R package provides functions for plotting genomic data | functions for plotting genomic data | is listed by: Debian | Free, Available for download, Freely available, | OMICS_15854 | https://sources.debian.org/src/r-bioc-geneplotter/ | SCR_024234 | 2026-08-05 10:48:00 | 0 | ||||||||
|
AnnotationHub Resource Report Resource Website 10+ mentions |
AnnotationHub (RRID:SCR_024227) | software toolkit, software resource | Software R package to provide a client for the Bioconductor AnnotationHub web resource. AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. | client, Bioconductor AnnotationHub web resource, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_29380 | https://sources.debian.org/src/r-bioc-annotationhub/ | SCR_024227 | 2026-08-05 10:48:01 | 24 | ||||||||
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hypergraph Resource Report Resource Website |
hypergraph (RRID:SCR_024240) | software toolkit, software resource | Software R package that implements some simple capabilities for representing and manipulating hypergraphs. | representing and manipulating hypergraphs, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-hypergraph/ | SCR_024240 | 2026-08-05 10:48:00 | 0 | |||||||||
|
htsfilter Resource Report Resource Website 1+ mentions |
htsfilter (RRID:SCR_024242) | software toolkit, software resource | Software R package implements filtering procedure for replicated transcriptome sequencing data based on global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions. | filtering procedure, replicated transcriptome sequencing data, global Jaccard similarity index, identify genes with low, constant levels of expression, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-htsfilter/ | SCR_024242 | 2026-08-05 10:48:01 | 5 | |||||||||
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multiassayexperiment Resource Report Resource Website |
multiassayexperiment (RRID:SCR_024245) | software toolkit, software resource | Software R package to harmonize data management of multiple experimental assays performed on overlapping set of specimens.Provides user experience by extending concepts from SummarizedExperiment, supporting open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames. Facilities are provided for reshaping data into wide and long formats for adaptability to graphing and downstream analysis. | harmonize data management, multiple experimental assays, overlapping set of specimens, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_19308 | https://sources.debian.org/src/r-bioc-multiassayexperiment/ | SCR_024245 | 2026-08-05 10:48:01 | 0 | ||||||||
|
mutationalpatterns Resource Report Resource Website 100+ mentions |
mutationalpatterns (RRID:SCR_024247) | software toolkit, software resource | Software R package provides set of flexible functions to evaluate and visualize multitude of mutational patterns in base substitution catalogues of e.g. healthy samples, tumour samples, or DNA-repair deficient cells. | evaluate and visualize multitude of mutational patterns, base substitution catalogues patterns, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-mutationalpatterns/ | SCR_024247 | 2026-08-05 10:48:00 | 220 | |||||||||
|
groHMM Resource Report Resource Website |
groHMM (RRID:SCR_024237) | software toolkit, software resource | Software R package for analysis of GRO-seq data. Used for identifying unannotated and cell type-specific transcription units from global run-on sequencing data | analysis of GRO-seq data, identifying unannotated and cell type-specific transcription units, global run-on sequencing data, | is listed by: Debian | PMID:26173492 | Free, Available for download, Freely available, | OMICS_07953 | https://sources.debian.org/src/r-bioc-grohmm/ | SCR_024237 | grohmm | 2026-08-05 10:48:00 | 0 | ||||||
|
genefilter Resource Report Resource Website 1+ mentions |
genefilter (RRID:SCR_024238) | software toolkit, software resource | Software R package provides some basic functions for filtering genes. | functions for filtering genes | is listed by: Debian | Free, Available for download, Freely available, | OMICS_29382 | https://sources.debian.org/src/r-bioc-genefilter/ | SCR_024238 | 2026-08-05 10:48:00 | 7 |
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