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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Starr Resource Report Resource Website |
Starr (RRID:SCR_001071) | software application, data processing software, data analysis software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software R package for the analysis of ChIP-chip data and Affymetrix tiling arrays. It provides functions for data import, quality assessment, and data visualization. The software provides tools for the efficient mapping of genomic sequences. | data import, quality, visualization, r, genomics, mapping, data analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
PMID:20398407 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00811 | SCR_001071 | 2026-02-15 09:18:02 | 0 | ||||||||
|
metahdep Resource Report Resource Website |
metahdep (RRID:SCR_001225) | metahdep | software application, data processing software, data analysis software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies. | differential expression, microarray, gene expression, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:19648140 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:metahdep, OMICS_02121 | https://bio.tools/metahdep | SCR_001225 | metahdep - Hierarchical Dependence in Meta-Analysis | 2026-02-15 09:18:04 | 0 | |||||
|
genArise Resource Report Resource Website 10+ mentions |
genArise (RRID:SCR_001346) | genArise | software application, data processing software, data analysis software, software resource | An easy to use software tool for dual color microarray data. Its GUI-Tk based environment lets any non-experienced user perform a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer. | microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Freely Available | OMICS_01993 | SCR_001346 | genArise - Microarray Analysis tool | 2026-02-15 09:18:05 | 22 | |||||||
|
categoryCompare Resource Report Resource Website 1+ mentions |
categoryCompare (RRID:SCR_001223) | categoryCompare | software application, data processing software, data analysis software, software resource | A software package for meta-analysis of high-throughput experiments using feature annotations. It calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested). | annotation, go, gene expression, multiple comparison, pathway, gene |
uses: Cytoscape is listed by: OMICtools is related to: Gene Ontology is related to: CRAN has parent organization: Bioconductor |
PMID:24808906 | Free, Available for download, Freely available | OMICS_02122 | SCR_001223 | categoryCompare - Meta-analysis of high-throughput experiments using feature annotations | 2026-02-15 09:18:04 | 9 | ||||||
|
MinimumDistance Resource Report Resource Website |
MinimumDistance (RRID:SCR_001260) | MinimumDistance | software application, data processing software, data analysis software, software resource | Software package for analysis of de novo copy number variants in trios from high-dimensional genotyping platforms. | copy number variation, microarray, snp |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02066 | SCR_001260 | MinimumDistance - A package for de novo CNV detection in case-parent trios | 2026-02-15 09:18:04 | 0 | |||||||
|
plateCore Resource Report Resource Website |
plateCore (RRID:SCR_001743) | data or information resource, database, software resource | Software that provides basic S4 data structures and routines for analyzing plate based flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19956418 | Free, Available for download, Freely available | OMICS_05641 | http://www.bioconductor.org/packages/release/bioc/html/plateCore.html | SCR_001743 | plateCore - Statistical tools and data structures for plate-based flow cytometry | 2026-02-15 09:18:10 | 0 | ||||||
|
ascend Resource Report Resource Website 1+ mentions |
ascend (RRID:SCR_017257) | software application, data processing software, data analysis software, software resource | Software R package for analysis of single cell RNA-seq expression, normalization and differential expression data. Provides framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression, and visualization functions. | analysis, single, cell, RNAseq, expression, normalization, data, gene, filtering, quality, control, dimension, reduction, clustering, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: CRAN is related to: Bioconductor |
PMID:31505654 | Free, Available for download, Freely available | biotools:ascend | https://bio.tools/ascend | SCR_017257 | Normalization and Differential expression, ASCEND, Analysis of Single Cell Expression | 2026-02-15 09:22:00 | 2 | ||||||
|
GEO2R Resource Report Resource Website 50+ mentions |
GEO2R (RRID:SCR_016569) | software application, data processing software, data analysis software, software resource | 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 | 2026-02-15 09:21:08 | 58 | ||||||||
|
riboSeqR Resource Report Resource Website 1+ mentions |
riboSeqR (RRID:SCR_016947) | software application, data processing software, data analysis software, software resource | 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 | 2026-02-15 09:21:56 | 4 | ||||||||||
|
scran Resource Report Resource Website 50+ mentions |
scran (RRID:SCR_016944) | SCRAN | software application, data processing software, data analysis software, software resource | 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 | 2026-02-15 09:21:52 | 92 | ||||
|
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 | ||||||
|
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 | |||||||
|
DEGreport Resource Report Resource Website 10+ mentions |
DEGreport (RRID:SCR_018941) | software application, data processing software, data analysis software, software resource | 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 | 2026-02-15 09:21:44 | 16 | |||||||||
|
biomaRt Resource Report Resource Website 1000+ mentions |
biomaRt (RRID:SCR_019214) | software application, data processing software, data analysis software, software resource | Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. | BioMart databases, Bioconductor, data analysis, BioMart data integration, gene annotation, gene product identifiers annotation, gene symbol retrival, chromosomal coordinates retrival, genomic sequence retrival, nucleotide polimorphism information, , bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: BioMart Project is related to: BioMart MartView is related to: Entrez Gene is related to: Affymetrix is related to: Gene Ontology is related to: OMIM is related to: Affymetrix |
PMID:16082012 | Free, Available for download, Freely available | biotools:biomart | https://bio.tools/biomart | SCR_019214 | biomaRt v 2.42.1 | 2026-02-15 09:22:28 | 2638 | ||||||
|
r3Cseq Resource Report Resource Website 10+ mentions |
r3Cseq (RRID:SCR_003198) | r3Cseq | software application, data processing software, data analysis software, software resource | An R/Bioconductor package to identify chromosomal interaction regions generated by chromosome conformation capture (3C) coupled to next-generation sequencing (NGS), a technique termed 3C-seq. It performs data analysis for a number of different experimental designs, as it can analyze 3C-seq data with or without a control experiment and it can be used to facilitate data analysis for experiments with multiple replicates. The r3Cseq package provides functions to perform data normalization, statistical analysis for cis/trans interactions and visualization in order to help scientists identify genomic regions that physically interact with the given viewpoints of interest. This tool greatly facilitates hypothesis generation and the interpretation of experimental results. | next-generation sequencing, genomic, interaction, chromosome conformation capture, chromosome, 3c-seq, r |
is listed by: OMICtools has parent organization: University of Bergen; Bergen; Norway has parent organization: Bioconductor |
PMID:23671339 | Free, Freely available | OMICS_01560 | SCR_003198 | 2026-02-15 09:18:28 | 24 | |||||||
|
EasyqpcR Resource Report Resource Website 1+ mentions |
EasyqpcR (RRID:SCR_003406) | EasyqpcR | software application, data processing software, data analysis software, software resource | Software package for low-throughput real-time quantitative PCR data analysis. The package allows you to import easily qPCR data files. Thereafter, you can calculate amplification efficiencies, relative quantities and their standard errors, normalization factors based on the best reference genes choosen (using the SLqPCR package), and then the normalized relative quantities, the NRQs scaled to your control and their standard errors. | qpcr, gene expression |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02313 | https://www.bioconductor.org/packages//2.13/bioc/html/EasyqpcR.html | SCR_003406 | 2026-02-15 09:18:30 | 9 | |||||||
|
metaSeq Resource Report Resource Website |
metaSeq (RRID:SCR_000056) | metaSeq | software application, data processing software, data analysis software, software resource | 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 | 2026-02-15 09:17:51 | 0 | ||||||||
|
Rsubread Resource Report Resource Website 100+ mentions |
Rsubread (RRID:SCR_016945) | software application, data processing software, data analysis software, image analysis software, software resource, alignment 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 | 2026-02-16 09:49:07 | 188 | ||||||
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Biostrings Resource Report Resource Website 100+ mentions |
Biostrings (RRID:SCR_016949) | software application, data processing software, sequence analysis software, data analysis software, 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 | 2026-02-16 09:49:07 | 167 |
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