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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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mergeomics Resource Report Resource Website 1+ mentions |
mergeomics (RRID:SCR_024244) | software toolkit, software resource | 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 | 2026-08-09 09:08:25 | 2 | |||||||
|
metagenomeseq Resource Report Resource Website 100+ mentions |
metagenomeseq (RRID:SCR_024246) | software toolkit, software resource | 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 | 2026-08-09 09:08:49 | 243 | |||||||||
|
gviz Resource Report Resource Website 10+ mentions |
gviz (RRID:SCR_024239) | software toolkit, software resource | 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 | 2026-08-09 09:09:00 | 46 | ||||||||
|
psychometric Resource Report Resource Website 1+ mentions |
psychometric (RRID:SCR_024295) | software toolkit, software resource | 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 | 2026-08-09 09:08:26 | 1 | ||||||||
|
rniftilib Resource Report Resource Website |
rniftilib (RRID:SCR_024296) | software toolkit, software resource | 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 | 2026-08-09 09:09:02 | 0 | |||||||||
|
rook Resource Report Resource Website |
rook (RRID:SCR_024298) | software toolkit, software resource | 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 | 2026-08-09 09:08:26 | 0 | |||||||||
|
robustrankaggreg Resource Report Resource Website 1+ mentions |
robustrankaggreg (RRID:SCR_024299) | RRA | software toolkit, software resource | 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 | 2026-08-09 09:09:02 | 4 | |||||||
|
rncl Resource Report Resource Website |
rncl (RRID:SCR_024290) | software toolkit, software resource | 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 | 2026-08-09 09:09:02 | 0 | |||||||||
|
hms Resource Report Resource Website |
hms (RRID:SCR_024294) | software toolkit, software resource | 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 | 2026-08-09 09:08:51 | 0 | |||||||||
|
Thermo Scientific Maps Software Resource Report Resource Website 1+ mentions |
Thermo Scientific Maps Software (RRID:SCR_024446) | software toolkit, software resource | Correlative electron microscopy and cross-platform imaging automation software. Imaging and correlative workflow software suite compatible with full line of Thermo Scientific SEM, DualBeam (FIB SEM) and TEM platforms. | Correlative electron microscopy, cross-platform imaging automation, imaging and correlative workflow, | Restricted | SCR_024446 | Maps Software | 2026-08-09 09:09:03 | 5 | ||||||||||
|
sambamba Resource Report Resource Website 50+ mentions |
sambamba (RRID:SCR_024328) | software toolkit, software resource | 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 | 2026-08-09 09:08:26 | 59 | |||||||
|
seq-seq-pan Resource Report Resource Website |
seq-seq-pan (RRID:SCR_024343) | software toolkit, software resource | 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 | 2026-08-09 09:08:52 | 0 | ||||||||
|
SIMA Resource Report Resource Website 1+ mentions |
SIMA (RRID:SCR_024466) | software toolkit, software resource | Software Python package for analysis of dynamic fluorescence microscopy data. | fluorescence microscopy data, microscopy data analysis, | Free, Available for download, Freely available | SCR_024466 | 2026-08-09 09:09:04 | 2 | |||||||||||
|
microbiome Resource Report Resource Website 10+ mentions |
microbiome (RRID:SCR_024699) | software toolkit, software resource | Software R package for use in microbiome analysis. Used to provide comprehensive collection of tools and tutorials, with particular focus on amplicon sequencing data. | amplicon sequencing data, microbiome analysis, | is listed by: Bioconductor | Free, Available for download, Freely available | https://microbiome.github.io/tutorials/, https://github.com/microbiome/microbiome/, | SCR_024699 | 2026-08-09 09:09:05 | 22 | |||||||||
|
genetics Resource Report Resource Website 1+ mentions |
genetics (RRID:SCR_024279) | software toolkit, software resource | Software R package for handling genetic data. Includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium. | handling genetic data, allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-genetics/ | SCR_024279 | 2026-08-09 09:08:50 | 3 | |||||||||
|
scCustomize Resource Report Resource Website 100+ mentions |
scCustomize (RRID:SCR_024675) | software toolkit, software resource | Software R package for custom visualizations and functions for streamlined analyses of single cell sequencing. | custom visualizations, single cell sequencing, single cell sequencing analysis, | is listed by: CRAN | Free, Available for download, Freely available | https://CRAN.R-project.org/package=scCustomize, https://github.com/samuel-marsh/scCustomize, https://doi.org/10.5281/zenodo.5706430 | SCR_024675 | 2026-08-09 09:08:58 | 100 | |||||||||
|
readseq Resource Report Resource Website 1+ mentions |
readseq (RRID:SCR_024313) | software toolkit, software resource | 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 | 2026-08-09 09:08:26 | 6 | |||||||||
|
rsvd Resource Report Resource Website |
rsvd (RRID:SCR_024303) | software toolkit, software resource | 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 | 2026-08-09 09:08:51 | 0 | |||||||
|
riskRegression Resource Report Resource Website 10+ mentions |
riskRegression (RRID:SCR_024424) | software toolkit, software resource | Software R package provides risk regression models and prediction scores for survival analysis with competing risks. | risk prediction, risk regression models, prediction scores, survival analysis, competing risks, | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/tagteam/riskRegression | SCR_024424 | 2026-08-09 09:08:54 | 15 | |||||||||
|
surveillance Resource Report Resource Website |
surveillance (RRID:SCR_024304) | software toolkit, software resource | Software R package for modeling and monitoring of time series of counts, proportions and categorical data, as well as for modeling of continuous-time point processes of epidemic phenomena. | modeling and monitoring of time series of counts, proportions and categorical data, modeling of continuous-time point processes, | is listed by: Debian | DOI:10.1007/s00180-007-0074-8 | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-surveillance/ | SCR_024304 | 2026-08-09 09:08:26 | 0 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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