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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-09-12 12:55:29 | 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 | 2026-09-12 12:55:30 | 5 | ||||||
|
TaLasso Resource Report Resource Website 1+ mentions |
TaLasso (RRID:SCR_001726) | TaLasso | analysis service resource, data analysis service, production service resource, service resource, software resource | Tool for quantification of human miRNA-mRNA Interactions. TaLasso is also available as Matlab or R code. | mirna, mrna, matlab, r, gene expression, gene |
is listed by: OMICtools has parent organization: Autonomous University of Madrid; Madrid; Spain |
PMID:22348024 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00417 | SCR_001726 | 2026-09-12 12:55:30 | 1 | |||||||
|
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 | 2026-09-12 12:55:30 | 49 | ||||||
|
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 | 2026-09-12 12:55:30 | 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 | 2026-09-12 12:55:30 | 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 | 2026-09-12 12:55:31 | 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 | 2026-09-12 12:55:31 | 25 | |||||
|
Prediction of Amyloid Structure Aggregation Resource Report Resource Website 100+ mentions |
Prediction of Amyloid Structure Aggregation (RRID:SCR_001768) | PASTA | analysis service resource, data analysis service, production service resource, service resource, software resource, web application | Online interface that utilizes an algorithm to predict the most aggregation-prone portions and the corresponding beta-strand inter-molecular pairing for a given input sequence. Users can paste the sequence into the interface and output the appropriate sequence. | protein aggregation, sequence, dna, rna, amyloid structure, protein analysis, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Padua; Padua; Italy |
Padova University Progetto di Ateneo CPDA121890; Italian Ministry for University and Research FIRB Futuro in Ricerca RBFR08ZSXY |
PMID:24848016 | Free, Freely available | biotools:pasta, OMICS_03861 | https://bio.tools/pasta | SCR_001768 | PASTA 2.0, Prediction of amyloid structure aggregation | 2026-09-12 12:55:31 | 180 | ||||
|
PLINK Resource Report Resource Website 10000+ mentions Issue |
PLINK (RRID:SCR_001757) | data analysis software, data processing software, software application, software resource, software toolkit | Open source whole genome association analysis toolset, designed to perform range of basic, large scale analyses in computationally efficient manner. Used for analysis of genotype/phenotype data. Through integration with gPLINK and Haploview, there is some support for subsequent visualization, annotation and storage of results. PLINK 1.9 is improved and second generation of the software. | gene, genetic, genomic, genotype, phenotype, copy number variant, whole-genome association, population, linkage analysis, whole-genome association study, data management, summary statistics, population stratification, association analysis, identity-by-descent estimation |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: Whap is related to: PLINK/SEQ is related to: Haploview is related to: MendelIHT.jl |
PMID:17701901 DOI:10.1086/519795 |
Free, Available for download, Freely Available | nlx_154200, OMICS_00206, SCR_021271 | https://zzz.bwh.harvard.edu/plink/, https://www.cog-genomics.org/plink/1.9/general_usage#cite, https://sources.debian.org/src/plink/ | http://pngu.mgh.harvard.edu/~purcell/plink/ | SCR_001757 | PLINK 1.9, PLINK/SEQ, plink - Whole genome association analysis toolset | 2026-09-12 12:55:30 | 16581 | |||||
|
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 | 2026-09-12 12:55:29 | 0 | ||||||
|
CQN Resource Report Resource Website 1+ mentions |
CQN (RRID:SCR_001786) | CQN | software resource | A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method. | rna-seq, differential expression, preprocessing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
PMID:22285995 | Free, Available for download, Freely available | OMICS_01949, biotools:cqn | https://bio.tools/cqn | SCR_001786 | Conditional Quantile Normalization | 2026-09-12 12:55:31 | 6 | |||||
|
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 | 2026-09-12 12:55:29 | 0 | |||||||
|
PoissonSeq Resource Report Resource Website 10+ mentions |
PoissonSeq (RRID:SCR_001784) | PoissonSeq | software resource | Software package that implements a method for normalization, testing, and false discovery rate estimation for RNA-sequencing data. | normalization, testing, false discovery rate, rna-seq |
is listed by: OMICtools has parent organization: Stanford University; Stanford; California |
PMID:22003245 | Free, Available for download, Freely available | OMICS_01950 | http://cran.r-project.org/web/packages/PoissonSeq/index.html | SCR_001784 | PoissonSeq: Significance analysis of sequencing data based on a Poisson log linear model | 2026-09-12 12:55:31 | 34 | |||||
|
MEME Suite - Motif-based sequence analysis tools Resource Report Resource Website 1000+ mentions |
MEME Suite - Motif-based sequence analysis tools (RRID:SCR_001783) | MEME Suite | analysis service resource, data analysis service, data analysis software, data or information resource, data processing software, database, production service resource, service resource, software application, software resource, source code | Suite of motif-based sequence analysis tools to discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences; search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN; compare a motif to all motifs in a database of motifs; associate motifs with Gene Ontology terms via their putative target genes, and analyze motif enrichment using SpaMo or CentriMo. Source code, binaries and a web server are freely available for noncommercial use. | gene ontology, motif, comparative genomics, dna regulatory motif, dna sequence, dna, gene, transcription factor, genome, protein, analysis, function analysis, comparison, cluster, enrichment analysis, sequence analysis, bio.tools, FASEB list |
lists: DREME is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Glam2 is related to: ANNOgesic is related to: memesuite-lite has parent organization: National Biomedical Computation Resource is parent organization of: GOMO - Gene Ontology for Motifs |
NCRR R01 RR021692 | PMID:19458158 DOI:10.1093/nar/gkl198 |
Free, Freely available | nif-0000-10298, biotools:meme_suite, OMICS_08103 | https://bio.tools/meme_suite | http://meme.sdsc.edu/meme4_6_1/intro.html, http://meme.nbcr.net/meme/, https://sources.debian.org/src/meme/ | SCR_001783 | The MEME Suite | 2026-09-12 12:55:31 | 2472 | |||
|
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 | 2026-09-12 12:55:31 | 16 | |||||||
|
TCC Resource Report Resource Website 10+ 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 | 2026-09-12 12:55:31 | 10 | ||||||
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CCAT Resource Report Resource Website 50+ mentions |
CCAT (RRID:SCR_001843) | CCAT | software resource | THIS RESOURCE IS OUT OF SERVICE, documented on April 5, 2017, A software package for the analysis of ChIP-seq data with negative control., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Genome Institute of Singapore; Singapore; Singapore |
PMID:20371496 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00428, biotools:ccat | https://bio.tools/ccat | SCR_001843 | Control based ChIP-Seq Analysis Tools | 2026-09-12 12:55:32 | 76 | |||||
|
GenABEL Resource Report Resource Website 500+ mentions |
GenABEL (RRID:SCR_001842) | software library, software resource, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. R software library for genome-wide association analysis for quantitative, binary and time-till-event traits. | r, genome-wide association, single nucleotide polymorphism |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: SoftCite |
Centre for Medical Systems Biology; Netherlands ; Netherlands Genomics Initiative ; Netherlands Organisation for Scientific Research ; Russian Foundation for Basic Research |
PMID:17384015 DOI:10.1186/1471-2105-11-134 DOI:10.1093/bioinformatics/btm108 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154328, OMICS_00234 | http://mga.bionet.nsc.ru/~yurii/ABEL/GenABEL/, https://cran.r-project.org/web/packages/GenABEL/index.html, https://sources.debian.org/src/probabel/ | SCR_001842 | GenABEL package, R/GENABEL | 2026-09-12 12:55:32 | 506 | |||||
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Alt Event Finder Resource Report Resource Website |
Alt Event Finder (RRID:SCR_001846) | Alt Event Finder | software resource | Software tool for deriving data-driven alternative splicing (AS) events from RNA-seq data. It analyses the transcripts built by Cufflinks or Scripture and outputs AS event annotations which is compatible with MISO. It can be used for annotating novel AS events from a well-annotated species such as human. It can also be used for species of which known AS event annotation is not available. The current release (v0.1) supports skipped exon events only. | alternative splicing, rna-seq, alternative splicing event, transcript, annotation, splicing regulation |
is listed by: OMICtools is related to: Cufflinks is related to: Scripture has parent organization: Indiana University; Indiana; USA |
PMID:23281921 | Free, Freely available | OMICS_01941 | SCR_001846 | Alt Event Finder: A tool for extracting alternative splicing events from RNA-seq data | 2026-09-12 12:55:32 | 0 |
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