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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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python-bx Resource Report Resource Website 10+ mentions |
python-bx (RRID:SCR_024202) | software library, software resource, software toolkit | Software Python library and associated set of scripts for rapid implementation of genome scale analyses. | rapid implementation of genome scale analyses, | is listed by: Debian | OMICS_18239 | https://sources.debian.org/src/python3-bx/ | SCR_024202 | 2026-09-19 12:56:20 | 49 | |||||||||
|
dynamicTreeCut Resource Report Resource Website 1+ mentions |
dynamicTreeCut (RRID:SCR_024280) | software resource, software toolkit | Software R package contains methods for detection of clusters in hierarchical clustering dendrograms. | clusters detection, hierarchical clustering dendrograms, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_23803 | https://sources.debian.org/src/r-cran-dynamictreecut/ | SCR_024280 | r-cran-dynamictreecut, dynamicTreeCut: Methods for Detection of Clusters in Hierarchical Clustering Dendrograms | 2026-09-19 12:56:22 | 6 | |||||||
|
preprocesscore Resource Report Resource Website 50+ mentions |
preprocesscore (RRID:SCR_024254) | software resource, software toolkit | Software library of core preprocessing routines. | core preprocessing routines, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-preprocesscore/ | SCR_024254 | 2026-09-19 12:56:21 | 63 | |||||||||
|
qusage Resource Report Resource Website 1+ mentions |
qusage (RRID:SCR_024255) | software resource, software toolkit | Software R package is implementation Quantitative Set Analysis for Gene Expression method. Used to provide faster, more accurate, and easier to understand test for gene expression studies. | test for gene expression studies, | is listed by: Debian | PMID:23921631 | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-qusage/ | SCR_024255 | Quantitative Set Analysis for Gene Expression | 2026-09-19 12:56:21 | 3 | |||||||
|
rsamtools Resource Report Resource Website 50+ mentions |
rsamtools (RRID:SCR_024257) | software resource, software toolkit | Software R package provides interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating Sequence Alignment Map, FASTA, binary variant call and compressed indexed tab-delimited files. | tabix interface, samtools interface, bcftools interface, Sequence Alignment Map manipulation, SAM manipulation, FASTA manipulation, binary variant call manipulation, compressed indexed tab delimited files manipulation, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-rsamtools/ | SCR_024257 | 2026-09-19 12:56:21 | 61 | |||||||||
|
savr Resource Report Resource Website |
savr (RRID:SCR_024258) | software resource, software toolkit | Software R package to parse Illumina Sequence Analysis Viewer files, access data, and generate QC plots. | parse Illumina Sequence Analysis Viewer files, access data, generate QC plots, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_15992 | https://sources.debian.org/src/r-bioc-savr/ | SCR_024258 | 2026-09-19 12:56:21 | 0 | ||||||||
|
nanostringqcpro Resource Report Resource Website 1+ mentions |
nanostringqcpro (RRID:SCR_024250) | software resource, software toolkit | Software R package to assess quality of NanoString mRNA gene expression data, to identify outlier probes and outlier samples. Provides different background subtraction and normalization approaches for this data. It outputs suggestions for flagging samples/probes and easily sharable html quality control output. | assess quality of NanoString mRNA gene expression data, identify outlier probes and outlier samples, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-nanostringqcpro/ | SCR_024250 | 2026-09-19 12:56:21 | 7 | |||||||||
|
pwmenrich Resource Report Resource Website 1+ mentions |
pwmenrich (RRID:SCR_024249) | software resource, software toolkit | Software toolkit of high level functions for DNA motif scanning and enrichment analysis built upon Biostrings. Used for PWM enrichment analysis of already known PWMs. Also implements high-level functions for PWM scanning and visualisation. | DNA motif scanning and enrichment analysis, Biostrings, PWM enrichment analysis, PWM scanning and visualisation, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-pwmenrich/ | SCR_024249 | 2026-09-19 12:56:21 | 3 | |||||||||
|
xvector Resource Report Resource Website |
xvector (RRID:SCR_024263) | software resource, software toolkit | Software R package provides memory efficient S4 classes for storing sequences externally. | provides memory efficient S4 classes, storing sequences externally, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-xvector/ | SCR_024263 | 2026-09-19 12:56:21 | 0 | |||||||||
|
BoolNet Resource Report Resource Website 1+ mentions |
BoolNet (RRID:SCR_024264) | software resource, software toolkit | Software R package provides functions to reconstruct, generate, and simulate synchronous, asynchronous, probabilistic, and temporal Boolean networks. Provides also functions to analyze and visualize attractors in Boolean networks. | reconstruct, generate, simulate, synchronous, asynchronous, probabilistic, temporal, Boolean networks, | is listed by: Debian | PMID:20378558 | Free, Available for download, Freely available, | OMICS_06963 | https://sources.debian.org/src/r-cran-boolnet/ | SCR_024264 | BoolNet: Construction, Simulation and Analysis of Boolean Networks, r-cran-boolnet | 2026-09-19 12:56:21 | 2 | ||||||
|
cmprsk Resource Report Resource Website 1+ mentions |
cmprsk (RRID:SCR_024265) | software resource, software toolkit | Software R package for estimation, testing and regression modeling of subdistribution functions in competing risks. | estimation, testing, regression modeling, subdistribution functions in competing risks, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-cmprsk/ | SCR_024265 | cmprsk: Subdistribution Analysis of Competing Risks, r-cran-cmprsk | 2026-09-19 12:56:21 | 3 | ||||||||
|
bio3d Resource Report Resource Website 100+ mentions |
bio3d (RRID:SCR_024266) | software resource, software toolkit | Softwar R package for comparative analysis of protein structures. Used to process, organize and explore protein structure, sequence and dynamics data. Used to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. Enables statistical and graphical power of R environment to work with biological sequence and structural data. | comparative analysis of protein structures, process protein structure, organize and explore protein structure, sequence and dynamics data, | is listed by: Debian | PMID:16940322 | Free, Available for download, Freely available, | OMICS_12577 | https://sources.debian.org/src/r-cran-bio3d/ | SCR_024266 | r-cran-bio3d, bio3d: Biological Structure Analysis | 2026-09-19 12:56:21 | 341 | ||||||
|
DoseFinding Resource Report Resource Website 1+ mentions |
DoseFinding (RRID:SCR_024268) | software resource, software toolkit | Software R package provides functions for design and analysis of dose finding experiments. Used for multiple contrast tests, fitting non-linear dose-response models, calculating optimal designs and implementation of MCPMod methodology. | dose finding experiments design and analysis functions, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-dosefinding/ | SCR_024268 | DoseFinding: Planning and Analyzing Dose Finding Experiments, r-cran-dosefinding | 2026-09-19 12:56:21 | 1 | ||||||||
|
distory Resource Report Resource Website |
distory (RRID:SCR_024269) | software resource, software toolkit | Software R package for geodesic distance between phylogenetic trees and associated functions. | geodesic distance, phylogenetic trees, associated functions, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_33012 | https://sources.debian.org/src/r-cran-distory/ | SCR_024269 | distory: Distance Between Phylogenetic Histories, r-cran-distory | 2026-09-19 12:56:21 | 0 | |||||||
|
alakazam Resource Report Resource Website 1+ mentions |
alakazam (RRID:SCR_024261) | software resource, software toolkit | Software R package for high-throughput adaptive immune receptor repertoire sequencing analysis. In particular, immunoglobulin sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage. | high throughput adaptive immune receptor repertoire sequencing analysis, sequencing analysis, | is listed by: Debian | PMID:26069265 | Free, Available for download, Freely available, | OMICS_21399 | https://sources.debian.org/src/r-cran-alakazam/ | SCR_024261 | 2026-09-19 12:56:21 | 6 | |||||||
|
ade4 Resource Report Resource Website 10+ mentions |
ade4 (RRID:SCR_024259) | software resource, software toolkit | Software R package for multivariate data analysis. Used for analysis of one-table, two-table, three-table and K-table. | multivariate data analysis, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-ade4/ | SCR_024259 | 2026-09-19 12:56:21 | 20 | |||||||||
|
psignifit Resource Report Resource Website 1+ mentions |
psignifit (RRID:SCR_024196) | software library, software resource, software toolkit | Software toolbox to fit psychometric functions and to test hypotheses about psychometric data. | fit psychometric functions, test hypotheses, psychometric data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/psignifit/ | SCR_024196 | 2026-09-19 12:56:19 | 3 | |||||||||
|
bridgedbr Resource Report Resource Website |
bridgedbr (RRID:SCR_024231) | software resource, software toolkit | Software R pacakge provides functions and load identifier mapping databases in R. Uses GitHub, Zenodo, and Figshare if you use this package to download identifier mappings files. | R functions, load identifier mapping databases in R, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-bridgedbr/ | SCR_024231 | 2026-09-19 12:56:20 | 0 | |||||||||
|
CNEr Resource Report Resource Website |
CNEr (RRID:SCR_024233) | software resource, software toolkit | Software R package provides large scale identification and advanced visualization of sets of conserved noncoding elements. | identification and advanced visualization of sets, conserved noncoding elements, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_33013 | https://sources.debian.org/src/r-bioc-cner/ | SCR_024233 | 2026-09-19 12:56:20 | 0 | ||||||||
|
genomeinfodb Resource Report Resource Website 1+ mentions |
genomeinfodb (RRID:SCR_024235) | software resource, software toolkit | Software R package contains data and functions that define and allow translation between different chromosome sequence naming conventions, including function that attempts to place sequence names in their natural, rather than lexicographic order. | data and functions, translation between different chromosome sequence naming conventions, chromosome sequence naming conventions, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-genomeinfodb/ | SCR_024235 | 2026-09-19 12:56:20 | 4 |
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