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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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OLIN Resource Report Resource Website 10+ mentions |
OLIN (RRID:SCR_001304) | OLIN | software resource | Software functions for normalization of two-color microarrays by optimised local regression and for detection of artifacts in microarray data. | r, normalization, visualization, quality control, two-channel, microarray, preprocessing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Humboldt University of Berlin; Berlin; Germany has parent organization: Bioconductor |
PMID:15585527 | Free, Available for download, Freely available | biotools:olin, OMICS_02029 | http://itb.biologie.hu-berlin.de/~futschik/software/R/OLIN/index.html | SCR_001304 | Optimised Local Intensity-dependent Normalisation | 2026-08-01 12:01:37 | 18 | |||||
|
qcmetrics Resource Report Resource Website 1+ mentions |
qcmetrics (RRID:SCR_001303) | qcmetrics | software resource | Software package that provides a framework for generic quality control of data. It permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in various formats. | mass spectrometry, microarray, proteomics, quality control, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02032, biotools:qcmetrics, BioTools:qcmetrics | https://bio.tools/qcmetrics, https://bio.tools/qcmetrics, https://bio.tools/qcmetrics | SCR_001303 | qcmetrics - A Framework for Quality Control | 2026-08-01 12:01:47 | 1 | ||||||
|
DEXUS Resource Report Resource Website 1+ mentions |
DEXUS (RRID:SCR_001309) | DEXUS | software resource | Software package that identifies differentially expressed genes in RNA-Seq data under all possible study designs such as studies without replicates, without sample groups, and with unknown conditions. It works also for known conditions, for example for RNA-Seq data with two or multiple conditions. RNA-Seq read count data can be provided both by the S4 class Count Data Set and by read count matrices. Differentially expressed transcripts can be visualized by heatmaps, in which unknown conditions, replicates, and samples groups are also indicated. This software is fast since the core algorithm is written in C. For very large data sets, a parallel version of DEXUS is provided in this package. DEXUS is a statistical model that is selected in a Bayesian framework by an EM algorithm. It does not need replicates to detect differentially expressed transcripts, since the replicates (or conditions) are estimated by the EM method for each transcript. The method provides an informative/non-informative value to extract differentially expressed transcripts at a desired significance level or power. | classification, differential expression, gene expression, hapmap, quality control, rna-seq, sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24049071 | Free, Available for download, Freely available | biotools:dexus, OMICS_02024 | http://www.bioconductor.org/packages/release/bioc/html/dexus.html | SCR_001309 | DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates | 2026-08-01 12:01:47 | 1 | |||||
|
CisGenome Resource Report Resource Website 50+ mentions |
CisGenome (RRID:SCR_001558) | data analysis tool | Integrated software tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis. | sequencing software, chip seq, downstream analysis, chip analysis, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian works with: TileMap |
PMID:18978777 | Free, Available for download, Freely available | OMICS_00423, biotools:cisgenome | https://bio.tools/cisgenome | http://biogibbs.stanford.edu/~jihk/CisGenome/index.htm | SCR_001558 | CisGenome v2.0 | 2026-08-01 12:01:44 | 82 | |||||
|
vsn Resource Report Resource Website 1+ mentions |
vsn (RRID:SCR_001459) | vsn | software resource | Software package that implements a method for normalizing microarray intensities, both between colours within array, and between arrays. The method uses a robust variant of the maximum-likelihood estimator for the stochastic model of microarray data described in the references. The model incorporates data calibration (a.k.a. normalization), a model for the dependence of the variance on the mean intensity, and a variance stabilizing data transformation. Differences between transformed intensities are analogous to normalized log-ratios. However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription. | microarray, preprocessing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: European Bioinformatics Institute |
Free, Available for download, Freely available | OMICS_01977, biotools:vsn | https://bio.tools/vsn | SCR_001459 | vsn - Variance stabilization and calibration for microarray data | 2026-08-01 12:01:52 | 5 | ||||||
|
CytoSPADE Resource Report Resource Website 1+ mentions |
CytoSPADE (RRID:SCR_001457) | software resource | Cytoscape plugin that provides a high-performance implementation of an interface for the Spanning-tree Progression Analysis of Density-normalized Events (SPADE) algorithm for tree-based analysis and visualization of high-dimensional cytometry data. | plugin, mac os x, unix/linux, windows, c++, java, r |
uses: Cytoscape is listed by: OMICtools has parent organization: Stanford University; Stanford; California is a plug in for: Cytoscape |
PMID:22782546 | Free, Available for download, Freely available | OMICS_05644 | http://cytospade.org/ | SCR_001457 | CytoSPADE: Cytoscape-driven Spanning tree Progression of Density normalized Events, CytoSPADE Cytoscape Plugin for SPADE, Cytoscape-driven Spanning tree Progression of Density normalized Events | 2026-08-01 12:01:41 | 2 | ||||||
|
BACContigEditor Resource Report Resource Website |
BACContigEditor (RRID:SCR_001617) | BACContigEditor | software resource | A simple sequence alignment editing tool, written in Java. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_00875 | SCR_001617 | 2026-08-01 12:01:57 | 0 | ||||||||
|
Enriched Domain Detector Resource Report Resource Website 1+ mentions |
Enriched Domain Detector (RRID:SCR_001693) | EDD | software resource | A ChIP-seq peak caller for detection of megabase domains of enrichment. | standalone software, unix/linux, mac os x | is listed by: OMICtools | PMID:24782521 | Free, Available for download, Freely available | OMICS_03964 | SCR_001693 | EDD - Enriched Domain Detector | 2026-08-01 12:01:47 | 7 | ||||||
|
CNVrd2 Resource Report Resource Website 1+ mentions |
CNVrd2 (RRID:SCR_001723) | software resource | A software package that uses next-generation sequencing data to measure human gene copy number for multiple samples, indentify SNPs tagging copy number variants and detect copy number polymorphic genomic regions. | standalone software, illumina, unix/linux, mac os x, windows, r, clustering., copy number variation, coverage, linkage disequilibrium, snp, sequencing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23646200 | Free, Available for download, Freely available | OMICS_03924 | http://www.bioconductor.org/packages/release/bioc/html/CNVrd2.html, https://github.com/hoangtn/CNVrd2 | SCR_001723 | CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data | 2026-08-01 12:01:48 | 5 | ||||||
|
sSeq Resource Report Resource Website 10+ mentions |
sSeq (RRID:SCR_001719) | sSeq | software resource | Software package to discover the genes that are differentially expressed between two conditions in RNA-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial (NB) distribution using a shrinkage approach for dispersion estimation. The method of moment (MM) estimates for dispersion are shrunk towards an estimated target, which minimizes the average squared difference between the shrinkage estimates and the initial estimates. The exact per-gene probability under the NB model is calculated, and used to test the hypothesis that the expected expression of a gene in two conditions identically follow a NB distribution. | rna-seq, differential expression |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23589650 | Free, Available for download, Freely available | OMICS_01962 | SCR_001719 | sSeq - Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size | 2026-08-01 12:01:34 | 47 | ||||||
|
RNASeqBias Resource Report Resource Website |
RNASeqBias (RRID:SCR_001739) | RNASeqBias | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10th,2023. An R software package for detecting and correcting biases in RNA-Sequencing data. | rna-seq |
is listed by: OMICtools has parent organization: Yale School of Medicine; Connecticut; USA |
THIS RESOURCE IS NO LONGER IN SERVICE. | OMICS_01957 | SCR_001739 | 2026-08-01 12:01:48 | 0 | ||||||||
|
pairedBayes Resource Report Resource Website 1+ mentions |
pairedBayes (RRID:SCR_001738) | pairedBayes | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10th,2023. An R code for Bayesian modeling of paired RNA-seq experiments. | r, rna-seq |
is listed by: OMICtools has parent organization: Yale School of Medicine; Connecticut; USA |
THIS RESOURCE IS NO LONGER IN SERVICE. | OMICS_01958 | SCR_001738 | 2026-08-01 12:02:00 | 1 | ||||||||
|
DNACLUST Resource Report Resource Website 1+ mentions |
DNACLUST (RRID:SCR_001771) | software resource | Software program for clustering large number of short similar DNA sequences. It was originally designed for clustering targeted 16S rRNA pyrosequencing reads. | cluster, dna sequence, gene, 16s rrna pyrosequencing read, microbiome |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian has parent organization: SourceForge |
PMID:21718538 DOI:10.1186/1471-2105-12-271 |
Free, Available for download, Freely available | OMICS_01955 | https://sources.debian.org/src/dnaclust/ | SCR_001771 | DNAClust | 2026-08-01 12:02:02 | 9 | ||||||
|
InterMine Resource Report Resource Website 10+ mentions |
InterMine (RRID:SCR_001772) | software resource | An open source data warehouse system built for the integration and analysis of complex biological data that enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding data. InterMine includes a user-friendly web interface that works "out of the box" and can be easily customized for specific needs, as well as a powerful, scriptable web-service API to allow programmatic access to data. | mac os x, unix/linux, windows, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Cambridge; Cambridge; United Kingdom |
Wellcome Trust | PMID:24753429 | Free, Freely available | OMICS_03840, biotools:intermine | https://github.com/intermine/intermine, https://bio.tools/intermine | http://intermine.github.io/intermine.org/ | SCR_001772 | 2026-08-01 12:01:50 | 22 | |||||
|
unifiedWMWqPCR Resource Report Resource Website |
unifiedWMWqPCR (RRID:SCR_001706) | software resource | Software package that implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data. | standalone software, mac os x, unix/linux, windows, r, gene expression, microtitre plate assay, qpcr, differential expression, multiple comparison, quality control, visualization, qpcr, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24794933 | Free, Available for download, Freely available | OMICS_03937, biotools:unifiedwmwqpcr | https://bio.tools/unifiedwmwqpcr | SCR_001706 | unifiedWMWqPCR - Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data | 2026-08-01 12:02:00 | 0 | ||||||
|
rlsim Resource Report Resource Website |
rlsim (RRID:SCR_001703) | rlsim | software resource | Software package for simulating RNA-seq library preparation with parameter estimation. | rna-seq |
is listed by: OMICtools has parent organization: European Bioinformatics Institute |
Free, Available for download, Freely available | OMICS_01965 | SCR_001703 | rlsim - a package for simulating RNA-seq library preparation with parameter estimation | 2026-08-01 12:01:47 | 0 | |||||||
|
RSVSim Resource Report Resource Website 10+ mentions |
RSVSim (RRID:SCR_001777) | software resource | A software package for the simulation of deletions, insertions, inversions, tandem duplications and translocations of various sizes in any genome available as FASTA-file or data package in R. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates. | unix/linux, mac os x, windows, r, sequencing, structural variation |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23620362 | Free, Available for download, Freely available | OMICS_03822 | SCR_001777 | RSVSim: an R/Bioconductor package for the simulation of structural variations | 2026-08-01 12:01:50 | 16 | |||||||
|
TCC Resource Report Resource Website 1+ mentions |
TCC (RRID:SCR_001779) | TCC | software resource | An R package that provides a series of functions for differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES). The basic idea of DEGES is that potential differentially expressed genes or transcripts (DEGs) among compared samples should be removed before data normalization to obtain a well-ranked gene list where true DEGs are top-ranked and non-DEGs are bottom ranked. This can be done by performing a multi-step normalization strategy (called DEGES for DEG elimination strategy). A major characteristic of TCC is to provide the robust normalization methods for several kinds of count data (two-group with or without replicates, multi-group/multi-factor, and so on) by virtue of the use of combinations of functions in other sophisticated packages (especially edgeR, DESeq, and baySeq). | rna-seq, differential expression, high throughput sequencing |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: University of Tokyo; Tokyo; Japan |
PMID:23837715 | Free, Available for download, Freely available | OMICS_01952 | SCR_001779 | Tag Count Comparison, TCC: Differential expression analysis for tag count data with robust normalization strategies | 2026-08-01 12:01:35 | 9 | ||||||
|
EDASeq Resource Report Resource Website 100+ mentions |
EDASeq (RRID:SCR_006751) | EDASeq | software resource | Software for numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | data analysis, normalization, rna-seq |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: National Cancer Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01231 | SCR_006751 | EDASeq: Exploratory Data Analysis and Normalization for RNA-Seq data | 2026-08-01 12:03:12 | 254 | |||||||
|
mubiomics Resource Report Resource Website 1+ mentions |
mubiomics (RRID:SCR_006785) | mubiomics | software resource | A set of scripts (mostly python) for processing reads generated by the Roche 454 or Illumina next-gen sequencing platforms. Included are quality control, read demultiplexing and microbiome characterisation scripts for use with usearch, pplacer and RDP classifier. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01059 | SCR_006785 | mubiomics - Scripts for processing next-gen sequencing data | 2026-08-01 12:03:13 | 3 |
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