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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Biostrings Resource Report Resource Website 100+ mentions |
Biostrings (RRID:SCR_016949) | software application, sequence analysis software, data processing software, software resource, data analysis software | Software package for efficient manipulation of biological strings. Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences. | manipulation, biological, string, memory, efficient, container, sequence, set, DNA, RNA, protein |
is used by: riboWaltz is listed by: Bioconductor is related to: R Project for Statistical Computing has parent organization: Stanford University; Stanford; California |
Free, Available for download, Freely available | https://web.stanford.edu/class/bios221/labs/biostrings/lab_1_biostrings.html | SCR_016949 | 2026-02-15 09:21:52 | 167 | |||||||||
|
ConsensusClusterPlus Resource Report Resource Website 100+ mentions |
ConsensusClusterPlus (RRID:SCR_016954) | software application, data processing software, data analysis software, software resource | Software written in R for determining cluster count and membership by stability evidence in unsupervised analysis. Provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset with item tracking, item consensus and cluster consensus plots. | cluster, count, stability, evidence, unsupervised, analysis, , bio.tools |
is listed by: Bioconductor is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
NCI F32CA142039; Thomas G. Labrecque Foundation ; NCI U24 CA126554 |
PMID:20427518 | Free, Available for download, Freely available | biotools:consensusclusterplus | https://bio.tools/consensusclusterplus | SCR_016954 | 2026-02-15 09:21:56 | 160 | ||||||
|
GenomicFeatures Resource Report Resource Website 50+ mentions |
GenomicFeatures (RRID:SCR_016960) | software application, data processing software, software resource, software toolkit, data analysis software | Software R package for making and manipulating transcript centric annotations. Used to download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database. | making, manipulating, transcript, centric, annotation, genomic, location, exon, cds, bio.tools |
is used by: riboWaltz is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
NHGRI P41 HG004059; NHGRI U41 HG004059; NHLBI R01 HL086601; NHLBI R01 HL093076; NHLBI R01 HL094635 |
PMID:23950696 | Free, Available for download, Freely available | biotools:genomicfeatures | https://bio.tools/genomicfeatures | SCR_016960 | 2026-02-15 09:21:12 | 65 | ||||||
|
FlowSOM Resource Report Resource Website 100+ mentions |
FlowSOM (RRID:SCR_016899) | software application, data visualization software, data processing software, software resource, data analysis software | Software tool to analyze Flow or mass cytometry data using a Self-Organizing Map. Used to obtain an overview of how all markers are behaving on all cells, and to detect subsets that might be missed otherwise. | flow, cytometry, data, analysis, self, organizing, map, marker, cell, detect, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is related to: R Project for Statistical Computing is a plug in for: FlowJo |
PMID:25573116 | Free, Available for download, Freely available | biotools:flowsom | https://bioconductor.org/packages/release/bioc/html/FlowSOM.html https://www.flowjo.com/exchange/#/plugin/profile?id=7 https://bio.tools/flowsom |
SCR_016899 | FlowSOM, Flow Self Organizing Map | 2026-02-15 09:21:50 | 106 | ||||||
|
ropls Resource Report Resource Website 10+ mentions |
ropls (RRID:SCR_016888) | R OPLS | software application, data processing software, data analysis software, software resource | Software R package for multivariate analysis and feature selection of omics data. Used for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables. | multivariate, analysis, feature, selection, omics, data, visualization, regression, classification, variable, exceedes, number, sample, multicollinearity, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | BioTools:ropls, biotools:ropls | https://bio.tools/ropls https://bio.tools/ropls https://bio.tools/ropls |
SCR_016888 | R Orthogonal Partial Least Squares | 2026-02-15 09:21:11 | 12 | ||||||
|
Goseq Resource Report Resource Website 100+ mentions |
Goseq (RRID:SCR_017052) | software application, data processing software, data analysis software, software resource | Software application for performing Gene Ontology analysis on RNAseq data and other length biased data. Used to reduce complexity and highlight biological processes in genome wide expression studies. | Gene, Ontology, analysis, RNAseq, data, sequencing, genome, expression, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
PMID:20132535 | Free, Available for download, Freely available | biotools:goseq | https://bio.tools/goseq | SCR_017052 | 2026-02-15 09:21:55 | 354 | |||||||
|
Genomic Ranges Resource Report Resource Website 1+ mentions |
Genomic Ranges (RRID:SCR_017051) | software application, data processing software, software resource, software toolkit, data analysis software | Software R package for computing and annotating genomic ranges. Used for storing and manipulating genomic intervals and variables defined along genome. | computing, annotating, genomic, range, storing, manipulating, interval, variable, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
NHGRI P41 HG004059; NHGRI U41 HG004059; NHLBI R01 HL086601; NHLBI R01 HL093076; NHLBI R01 HL094635 |
PMID:23950696 | Free, Available for download, Freely available | biotools:genomicranges | https://bio.tools/genomicranges | SCR_017051 | 2026-02-15 09:21:14 | 2 | ||||||
|
GeneNetworkBuilder Resource Report Resource Website 1+ mentions |
GeneNetworkBuilder (RRID:SCR_006455) | GeneNetworkBuilder | software application, software resource | Software application for discovering direct or indirect targets of transcription factors (TFs) using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, it generates a regulatory network of the TF. | transcription factor, graph, network, microarray, sequencing, chip-chip, chip-seq, gene expression, regulatory network, target |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 or greater | OMICS_00806, OMICS_01971 | http://www.bioconductor.org/packages/release/bioc/html/GeneNetworkBuilder.html | SCR_006455 | GeneNetworkBuilder - Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data | 2026-02-15 09:19:28 | 2 | ||||||
|
epialleleR Resource Report Resource Website 1+ mentions |
epialleleR (RRID:SCR_023913) | software toolkit, software resource | Software R package for calling hypermethylated variant epiallele frequencies at level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map files as input. Used for sensitive allele specific methylation analysis in next generation sequencing data. Used for sensitive detection, quantification and visualisation of mosaic epimutations in methylation sequencing data. | BAM files, binary alignment map files, allele specific methylation analysis, methylation sequencing data, next generation sequencing data, hypermethylated variant epiallele frequencies calling, | is listed by: Bioconductor | K.G.Jebsen Foundation ; Norwegian Cancer Society ; Norwegian Research Council |
DOI:10.1101/2022.06.30.498213 | Free, Available for download, Freely available | https://github.com/BBCG/epialleleR | SCR_023913 | 2026-02-15 09:23:28 | 1 | |||||||
|
KEGGgraph Resource Report Resource Website 10+ mentions |
KEGGgraph (RRID:SCR_023788) | software toolkit, software resource | Software R package interface between KEGG pathway and graph object as well as collection of tools to analyze, dissect and visualize these graphs. | Kyoto Encyclopedia of Genes and Genomes, KEGG, KEGG pathways, graph models, graph object, graphs visualization, | is listed by: Bioconductor | PMID:19307239 | Free, Available for download, Freely available | SCR_023788 | Kyoto Encyclopedia of Genes and Genomes graph | 2026-02-15 09:22:31 | 14 | ||||||||
|
CRCView Resource Report Resource Website |
CRCView (RRID:SCR_007092) | CRCView | service resource, analysis service resource, data analysis service, production service resource | Web-based microarray data analysis and visualization system powered by CRC, or Chinese Restaurant cluster, a Dirichlet process model-based clustering algorithm recently developed by Dr. Steve Qin. It also incorporates several gene expression analysis programs from Bioconductor, including GOStats, genefilter, and Heatplus. CRCView also installs from the Bioconductor system 78 annotation libraries of microarray chips for human (31), mouse (24), rat (14), zebrafish (1), chicken (1), Drosophila (3), Arabidopsis (2), Caenorhabditis elegans (1), and Xenopus Laevis (1). CRCView allows flexible input data format, automated model-based CRC clustering analysis, rich graphical illustration, and integrated Gene Ontology (GO)-based gene enrichment for efficient annotation and interpretation of clustering results. CRC has the following features comparing to other clustering tools: 1) able to infer number of clusters, 2) able to cluster genes displaying time-shifted and/or inverted correlations, 3) able to tolerate missing genotype data and 4) provide confidence measure for clusters generated. You need to register for an account in the system to store your data and analyses. The data and results can be visited again anytime you log in. | microarray, gene expression, cluster, gene, expression profile, data repository, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Bioconductor is related to: Gene Ontology has parent organization: University of Michigan; Ann Arbor; USA |
University of Michigan; Michigan; USA ; Institutional Fund ; NIH U013422; NIAID 1R21AI057875-01 |
PMID:17485426 | Registration required | biotools:crcview, nlx_99864 | https://bio.tools/crcview | http://helab.bioinformatics.med.umich.edu/crcview/ | SCR_007092 | Chinese Restaurant ClusterView | 2026-02-15 09:19:22 | 0 | |||
|
Orthology.eg.db Resource Report Resource Website 1+ mentions |
Orthology.eg.db (RRID:SCR_024740) | software toolkit, software resource | Software R package to provide orthology mappings between species, based on NCBI Gene IDs and NCBI orthology mappings. | orthology mappings between species, NCBI Gene IDs, NCBI orthology mappings, | is listed by: Bioconductor | Free, Available for download, Freely available | SCR_024740 | 2026-02-15 09:23:36 | 1 | ||||||||||
|
ExperimentHub Resource Report Resource Website 1+ mentions |
ExperimentHub (RRID:SCR_024820) | software toolkit, software resource | Software R package provides central location where curated data from experiments, publications or training courses can be accessed. | data access, curated data from experiments, publications data, training courses data, | is listed by: Bioconductor | Free, Available for download, Freely available | SCR_024820 | 2026-02-15 09:23:38 | 2 |
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