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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Extending Guilt by Association by Degree Resource Report Resource Website 1+ mentions |
Extending Guilt by Association by Degree (RRID:SCR_018427) | EGAD | data processing software, data analysis software, software toolkit, software application, software resource | Software package implements series of highly efficient tools to calculate functional properties of networks based on guilt by association methods. Ultra fast functional analysis of gene networks. | Extending guilt, association by degree, functional properties calculation, guilt network, association method, functional analysis, gene network | is listed by: Bioconductor | Free, Available for download, Freely available | SCR_018427 | EGAD Bioconductor, Extending guilt by association by degree | 2026-02-13 10:58:21 | 6 | ||||||||
|
EnhancedVolcano Resource Report Resource Website 100+ mentions |
EnhancedVolcano (RRID:SCR_018931) | data visualization software, software resource, data processing software, software application | Software R package to produce publication ready volcano plots with enhanced colouring and labeling. Used to visualise results of differential expression analyses. | Publication ready plot, enhanced coloring, enhanced labeling, data visualisation, differential expression analyses, plot, volcano plot |
uses: ggplot2 uses: ggrepel is listed by: Bioconductor |
Free, Available for download, Freely available | https://github.com/kevinblighe/EnhancedVolcano | SCR_018931 | 2026-02-13 10:58:17 | 469 | |||||||||
|
DEGreport Resource Report Resource Website 10+ mentions |
DEGreport (RRID:SCR_018941) | data analysis software, software resource, data processing software, software application | Software R package for creation of HTML report of differential expression analyses of count data. Integrates some of code mentioned in DESeq2 and edgeR vignettes, and reports ranked list of genes according to fold changes mean and variability for each selected gene. | HTML report creation, differential expression analyses, count data, code integration, gene list report | is listed by: Bioconductor | Free, Available for download, Freely available | http://lpantano.github.io/DEGreport | SCR_018941 | 2026-02-13 10:58:19 | 16 | |||||||||
|
GEO2R Resource Report Resource Website 50+ mentions |
GEO2R (RRID:SCR_016569) | data analysis software, software resource, data processing software, software application | Software as an interactive web tool to compare two or more groups of samples in a Gene Expression Omnibus (GEO) series regardless of data type and quality. Used to identify genes that are differentially expressed across experimental conditions. Results are presented as a table of genes ordered by significance. | compare, group, sample, gene, expression, omnibus, data, identify, differentially, expressed, across, condition, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Bioconductor is related to: GEOquery is related to: LIMMA |
Free, Available for download, Freely available | biotools:GEO2R | https://bio.tools/GEO2R | SCR_016569 | 2026-02-13 10:57:50 | 58 | ||||||||
|
VisR Resource Report Resource Website 1+ mentions |
VisR (RRID:SCR_016658) | VisR | data visualization software, data processing software, data analysis software, software toolkit, software application, software resource | Software as an R-based visual framework for analysis of sequencing datasets. Provides a framework for integrative and interactive analyses. | visual, framework, analysis, sequencing, data, dataset, integrative, interactive, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Bioconductor |
Michael Smith Foundation for Health Research ; Canadian Institutes of Health Research (CIHR) and Genome BC ; NSERC PGS-D |
PMID:26328469 | Free, Available for download, Freely available | biotools:VisR | https://bio.tools/VisR | SCR_016658 | VisRseq, VisR | 2026-02-13 10:57:51 | 5 | ||||
|
FlowSOM Resource Report Resource Website 100+ mentions |
FlowSOM (RRID:SCR_016899) | data visualization software, data processing software, data analysis software, software application, software resource | 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 | 2026-02-13 10:57:48 | 106 | ||||||
|
ropls Resource Report Resource Website 10+ mentions |
ropls (RRID:SCR_016888) | R OPLS | data analysis software, software resource, data processing software, software application | 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 | 2026-02-13 10:57:53 | 12 | ||||||
|
riboSeqR Resource Report Resource Website 1+ mentions |
riboSeqR (RRID:SCR_016947) | data analysis software, software resource, data processing software, software application | Software tool for analysis of sequencing data from ribosome profiling experiments. Used for plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments. | analysis, sequencing, data, ribosome, profiling, experiment, plotting, function, frameshift, detect, parsing |
is listed by: Bioconductor is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_016947 | 2026-02-13 10:57:53 | 4 | ||||||||||
|
Rsubread Resource Report Resource Website 100+ mentions |
Rsubread (RRID:SCR_016945) | data processing software, alignment software, data analysis software, software application, software resource, image analysis software | Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers. | sequence, alignment, counting, multi, seed, strategy, mapping, read, reference, genome, analysis, data, SNP, calling, mutation, discovery, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing is related to: Subread |
Australian National Health and Medical Research Council ; Victorian State Government Operational Infrastructure Support ; Australian Government |
PMID:23558742 | Free, Available for download, Freely available | biotools:rsubread | https://bio.tools/rsubread | SCR_016945 | 2026-02-13 10:57:54 | 188 | ||||||
|
scran Resource Report Resource Website 50+ mentions |
scran (RRID:SCR_016944) | SCRAN | data analysis software, software resource, data processing software, software application | Software package for low-level analyses of single-cell RNA-seq data. Used for quality control, data exploration and normalization, cell cycle phase assignment, identification of highly variable and correlated genes, clustering into subpopulations and marker gene detection. | low, level, analysis, scRNA-seq, data, normalization, cell, cycle, phase, gene, variable, correlation, cluster, subpopulation, marker, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
Cancer Research UK ; National Health and Medical Research Council of Australia ; EMBL |
PMID:27909575 | Free, Available for download, Freely available | biotools:scran | https://bio.tools/scran | SCR_016944 | Single-Cell Rna-seq data ANalysis, SCRAN | 2026-02-13 10:57:51 | 92 | ||||
|
Biostrings Resource Report Resource Website 100+ mentions |
Biostrings (RRID:SCR_016949) | sequence analysis software, data processing software, data analysis software, software application, software resource | 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 | 2026-02-13 10:57:51 | 167 | |||||||||
|
ConsensusClusterPlus Resource Report Resource Website 100+ mentions |
ConsensusClusterPlus (RRID:SCR_016954) | data analysis software, software resource, data processing software, software application | 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 | 2026-02-13 10:57:53 | 160 | ||||||
|
GenomicFeatures Resource Report Resource Website 50+ mentions |
GenomicFeatures (RRID:SCR_016960) | data processing software, data analysis software, software toolkit, software application, software resource | 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 | 2026-02-13 10:57:48 | 65 | ||||||
|
Goseq Resource Report Resource Website 100+ mentions |
Goseq (RRID:SCR_017052) | data analysis software, software resource, data processing software, software application | 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 | 2026-02-13 10:57:55 | 354 | |||||||
|
Genomic Ranges Resource Report Resource Website 1+ mentions |
Genomic Ranges (RRID:SCR_017051) | data processing software, data analysis software, software toolkit, software application, software resource | 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 | 2026-02-13 10:57:56 | 2 | ||||||
|
cn.FARMS Resource Report Resource Website |
cn.FARMS (RRID:SCR_000289) | cn.FARMS | data processing software, data analysis software, software toolkit, software application, software resource | Software R package for copy number variation analysis that allows analysis of the most common Affymetrix (250K-SNP6.0) array types and supports high-performance computing using snow and ff. | copy number variation analysis, copy number variation, microarray, affymetrix, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:21486749 | Free, Available for download, Freely available | biotools:cn.farms, OMICS_02060 | https://bio.tools/cn.farms | SCR_000289 | cn.farms - factor analysis for copy number estimation | 2026-02-13 10:54:38 | 0 | |||||
|
CorMut Resource Report Resource Website |
CorMut (RRID:SCR_000053) | sequence analysis software, data processing software, data analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software package for computing correlated mutations based on selection pressure. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network. | sequencing, correlated mutation, selection pressure, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: CRAN has parent organization: Bioconductor |
PMID:24681904 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_03636, biotools:cormut | https://bio.tools/cormut | SCR_000053 | CorMut - Detect the correlated mutations based on selection pressure | 2026-02-13 10:54:36 | 0 | ||||||
|
metaSeq Resource Report Resource Website |
metaSeq (RRID:SCR_000056) | metaSeq | data analysis software, software resource, data processing software, software application | Software package for meta-analysis of RNA-Seq count data in multiple studies. The probabilities by one-sided NOISeq are combined by Fisher's method or Stouffer's method. | differential expression, rna-seq, sequencing |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02123 | SCR_000056 | 2026-02-13 10:54:36 | 0 | ||||||||
|
factDesign Resource Report Resource Website |
factDesign (RRID:SCR_001330) | factDesign | data analysis software, software resource, data processing software, software application | Software package that provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection. | microarray, differential expression |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:18584033 | Free, Available for download, Freely available | OMICS_02008 | SCR_001330 | factDesign - Factorial designed microarray experiment analysis | 2026-02-13 10:54:50 | 0 | ||||||
|
spotSegmentation Resource Report Resource Website |
spotSegmentation (RRID:SCR_001298) | spotSegmentation | image processing software, software resource, data processing software, software application | Model-based software package for processing microarray images so as to estimate foreground and background intensities. The method starts with a very simple but effective automatic gridding method, and then proceeds in two steps. The first step applies model-based clustering to the distribution of pixel intensities, using the Bayesian Information Criterion (BIC) to choose the number of groups up to a maximum of three. The second step is spatial, finding the large spatially connected components in each cluster of pixels. The method thus combines the strengths of the histogram-based and spatial approaches. It deals effectively with inner holes in spots and with artifacts. It also provides a formal inferential basis for deciding when the spot is blank, namely when the BIC favors one group over two or three. | gridding, segmentation, microarray, preprocessing, quality control, two channel |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:15845656 | Free, Available for download, Freely available | OMICS_02037 | http://www.bioconductor.org/packages/release/bioc/html/spotSegmentation.html | SCR_001298 | 2026-02-13 10:54:50 | 0 |
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