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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
genomicalignments Resource Report Resource Website 100+ mentions |
genomicalignments (RRID:SCR_024236) | software resource, software toolkit | Software R package provides efficient containers for storing and manipulating short genomic alignments. This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments. | containers for storing and manipulating short genomic alignments, read counting, computing coverage, junction detection, working with nucleotide content of alignments. | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-genomicalignments/ | SCR_024236 | 2026-09-19 12:56:20 | 147 | |||||||||
|
BiocGenerics Resource Report Resource Website 10+ mentions |
BiocGenerics (RRID:SCR_024226) | software resource, software toolkit | Software R package defines many S4 generic functions used in Bioconductor. | S4 generic functions used in Bioconductor, S4 generic functions, Bioconductor, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-biocgenerics/ | SCR_024226 | 2026-09-19 12:56:20 | 27 | |||||||||
|
biomformat Resource Report Resource Website |
biomformat (RRID:SCR_024228) | software resource, software toolkit | Software R package for interfacing with BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, limited support for writing biom-object back to biom-format file. | interfacing with BIOM format, reading biom-format files, accessing and subsetting data tables from biom object, writing biom-object back to biom-format file, |
is listed by: Debian is related to: python-biom-format |
Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-biomformat/ | SCR_024228 | 2026-09-19 12:56:20 | 0 | |||||||||
|
biovizBase Resource Report Resource Website |
biovizBase (RRID:SCR_024229) | software resource, software toolkit | Software R package to provide set of utilities, color schemes and conventions for genomic data. Used for various high-level packages for biological data visualization. | utilities, color schemes and conventions for genomic data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-biovizbase/ | SCR_024229 | 2026-09-19 12:56:20 | 0 | |||||||||
|
go.db Resource Report Resource Website 10+ mentions |
go.db (RRID:SCR_024241) | software resource, software toolkit | Software R package provides set of annotation maps describing entire Gene Ontology assembled using data from GO. | set of annotation maps, Gene Ontology, data from GO, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_22608 | https://sources.debian.org/src/r-bioc-go.db/ | SCR_024241 | 2026-09-19 12:56:20 | 44 | ||||||||
|
impute Resource Report Resource Website 1+ mentions |
impute (RRID:SCR_024243) | software resource, software toolkit | Software R package for imputation for microarray data. | imputation for microarray data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-impute/ | SCR_024243 | 2026-09-19 12:56:20 | 5 | |||||||||
|
mergeomics Resource Report Resource Website 1+ mentions |
mergeomics (RRID:SCR_024244) | software resource, software toolkit | Software R pacakage for multidimensional data integration to identify pathogenic perturbations to biological systems. Used for integrating multidimensional omics disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. Includes Marker set enrichment analysis and Weighted Key Driver Analysis parts. | integrating multidimensional omics disease associations, integrating functional genomics, integrating canonical pathways and gene-gene interaction networks, multidimensional data integration, identify pathogenic perturbations to biological systems, | is listed by: Debian | PMID:27814671 | Free, Available for download, Freely available, | OMICS_12862 | https://sources.debian.org/src/r-bioc-mergeomics/ | SCR_024244 | 2026-09-19 12:56:20 | 2 | |||||||
|
metagenomeseq Resource Report Resource Website 100+ mentions |
metagenomeseq (RRID:SCR_024246) | software resource, software toolkit | Software R package to determine features that are differentially abundant between two or more groups of multiple samples. Used to address the effects of both normalization and under-sampling of microbial communities on disease association detection and testing of feature correlations. | determine features that are differentially abundant, two or more groups of multiple samples, disease association detection, testing of feature correlations, | is listed by: Debian | OMICS_07813 | https://sources.debian.org/src/r-bioc-metagenomeseq/ | SCR_024246 | 2026-09-19 12:56:21 | 243 | |||||||||
|
gviz Resource Report Resource Website 10+ mentions |
gviz (RRID:SCR_024239) | software resource, software toolkit | Software R package to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. | genomic data analyses, perform live annotation queries, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_17191 | https://sources.debian.org/src/r-bioc-gviz/ | SCR_024239 | 2026-09-19 12:56:20 | 46 | ||||||||
|
psychometric Resource Report Resource Website 1+ mentions |
psychometric (RRID:SCR_024295) | software resource, software toolkit | Software R package for measurement theory, meta-analysis, reliability, item analysis, inter-rater reliability, classical utility, and correlation | psychometric theory, measurement theory, meta-analysis, reliability, item analysis, inter-rater reliability, classical utility, correlation | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-psychometric/ | SCR_024295 | Applied Psychometric Theory | 2026-09-19 12:56:22 | 1 | ||||||||
|
rniftilib Resource Report Resource Website |
rniftilib (RRID:SCR_024296) | software resource, software toolkit | Software R package provides R-interface to the NIfTI reference implementation the niftilib C-library. | R-interface, NIfTI reference implementation, niftilib C-library, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-rniftilib/ | SCR_024296 | 2026-09-19 12:56:22 | 0 | |||||||||
|
rSNP Guide Resource Report Resource Website 1+ mentions |
rSNP Guide (RRID:SCR_000087) | data or information resource, database | A system of databases which stores information on the influence of mutations in regulatory gene regions . This tool helps recognize protein binding sites that are being altered by mutation. It has four cross-linked sub databases that focus on specific aspects including: (1) the effect of single nucleotide mutations in regulatory gene regions and their interaction with nuclear proteins; (2) references to original publications on the subject; (3) the experimental details of these publications; and (4) the protocols of these experiments. This resource is aimed at providing information to further research on the influence of specific sequence alterations on disease susceptibility, drug resistance and healthcare. | database, single nucleotide mutations, RNA, DNA, nuclear proteins, protein binding sites, drug resistance, disease susceptibility, health care, regulatory gene regions, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Siberian Branch of the Russian Academy of Sciences; Novosibirsk; Russia |
Open Source | nif-0000-03428, biotools:rsnp_guide | https://bio.tools/rsnp_guide | SCR_000087 | rSNP Guide | 2026-09-19 12:56:25 | 1 | |||||||
|
rook Resource Report Resource Website |
rook (RRID:SCR_024298) | software resource, software toolkit | Web server for R with documented API to interface between R and the server. The documentation contains the Rook specification and details for building and running Rook applications. | web server for R, building and running Rook applications, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-rook/ | SCR_024298 | 2026-09-19 12:56:22 | 0 | |||||||||
|
robustrankaggreg Resource Report Resource Website 1+ mentions |
robustrankaggreg (RRID:SCR_024299) | RRA | software resource, software toolkit | Software R package for aggregating ranked lists, especially lists of genes. RRA method uses a probabilistic model for aggregation that is robust to noise and also facilitates the calculation of significance probabilities for all the elements in the final ranking. | aggregating ranked lists, lists of genes aggregation, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-robustrankaggreg/ | SCR_024299 | Robust Rank Aggregation | 2026-09-19 12:56:22 | 4 | |||||||
|
rncl Resource Report Resource Website |
rncl (RRID:SCR_024290) | software resource, software toolkit | Software R package provides interface to Nexus Class Library which allows parsing of NEXUS, Newick and other phylogenetic tree file formats. Provides elements of file that can be used to build phylogenetic objects such as ape's 'phylo' or phylobase's 'phylo4(d)'. | interface to Nexus Class Library, parsing of NEXUS, parsing of Newick, parsing phylogenetic tree file formats, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-rncl/ | SCR_024290 | 2026-09-19 12:56:22 | 0 | |||||||||
|
hms Resource Report Resource Website |
hms (RRID:SCR_024294) | software resource, software toolkit | Software R package implements S3 class for storing and formatting time-of-day values, based on the 'difftime' class. | storing and formatting time-of-day values, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-hms/ | SCR_024294 | 2026-09-19 12:56:22 | 0 | |||||||||
|
sambamba Resource Report Resource Website 50+ mentions |
sambamba (RRID:SCR_024328) | software resource, software toolkit | Software tools for working with SAM/BAM data | working with SAM/BAM data, | is listed by: Debian | PMID:25697820 | Free, Available for download, Freely available, | OMICS_07586 | https://sources.debian.org/src/sambamba/ | SCR_024328 | 2026-09-19 12:56:23 | 59 | |||||||
|
seq-seq-pan Resource Report Resource Website |
seq-seq-pan (RRID:SCR_024343) | software resource, software toolkit | Software workflow for SEQuential alignment of SEQuences to build PAN-genome data structure and whole-genome-alignment. | SEQuential alignment, SEQuences, build PAN-genome data structure, | is listed by: Debian | PMID:29334898 | Free, Available for download, Freely available, | https://sources.debian.org/src/seq-seq-pan/ | SCR_024343 | 2026-09-19 12:56:23 | 0 | ||||||||
|
readseq Resource Report Resource Website 1+ mentions |
readseq (RRID:SCR_024313) | software resource, software toolkit | Software package as Java based common sequence file format reader and sequence file manipulation. | Java, common sequence file format reader, sequence file manipulation, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/rdp-readseq/ | SCR_024313 | 2026-09-19 12:56:23 | 6 | |||||||||
|
rsvd Resource Report Resource Website |
rsvd (RRID:SCR_024303) | software resource, software toolkit | Software R package used to compute near optimal low-rank singular value decomposition of massive data sets with high accuracy. Provides several randomized matrix algorithms such as randomized singular value decomposition (rsvd), randomized principal component analysis (rpca), randomized robust principal component analysis (rrpca), randomized interpolative decomposition (rid), and the randomized CUR decomposition (rcur). In addition several plot functions are provided. | randomized singular value decomposition, singular value decomposition, compute optimal low-rank singular value decomposition, massive data sets, | is listed by: Debian | DOI:10.18637/jss.v089.i11 | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-rsvd/ | SCR_024303 | randomized singular value decomposition | 2026-09-19 12:56:22 | 0 |
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