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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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oneClickCGH Resource Report Resource Website |
oneClickCGH (RRID:SCR_000294) | oneClickCGH | software resource, data processing software, software application, data analysis software | Platform-independent array copy number analysis software that provides straightforward yet comprehensive detection and reporting of copy number changes. | array, comparative genomic hybridization, cytogenetics, copy number variant, copy number analysis, | is listed by: OMICtools | Restricted | OMICS_02050 | SCR_000294 | 2026-08-05 10:43:08 | 0 | ||||||||
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HighWire Press Resource Report Resource Website 1+ mentions |
HighWire Press (RRID:SCR_000761) | data or information resource, publisher, service resource, database | A division of the Stanford University Libraries, which produces the online versions of journals and other scholarly content. | biomedical, communication, images, interactivity, literature, multimedia, science, scientific, scientific literature databases and services, technology |
is listed by: OMICtools has parent organization: Stanford University; Stanford; California |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21191 | SCR_000761 | HighWire Press | 2026-08-05 10:43:14 | 6 | ||||||||
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BAIT Resource Report Resource Website 1+ mentions |
BAIT (RRID:SCR_000511) | BAIT | data processing software, software application, data visualization software, data analysis software, software resource | Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data. | create strand inheritance plots, strand-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24028793 | Free, Available for download, Freely available | biotools:bait, OMICS_01531 | https://bio.tools/bait | SCR_000511 | BAIT - Software to help analyse Strand-Seq data | 2026-08-05 10:43:11 | 1 | |||||
|
DDBJ Omics Archive Resource Report Resource Website |
DDBJ Omics Archive (RRID:SCR_000597) | DOR | data or information resource, data repository, database, storage service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between ArrayExpress at EBI and DOR in common MAGE-TAB format. Supports MIAME and MINSEQE-compliant data submissions. DOR issues accession numbers, E-DORD-n to experiment and A-DORD-n to array design. DOR exchanges public data with the EBI ArrayExpress in common MAGE-TAB format. Note: At present, DOR does not accept submissions. DDBJ will announce launch of DOR when it is ready. (2013/01/31) The data can be kept private until your paper is published. You can set the hold date for a maximum of 1 year and can change it. Registered records are released according to the Data Release Policy. | functional genomics, array, sequence |
is listed by: OMICtools is related to: ArrayExpress is related to: MIAME is related to: MINSEQE is related to: MAGE-TAB has parent organization: DNA DataBank of Japan (DDBJ) |
PMID:22110025 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01026 | http://trace.ddbj.nig.ac.jp/dor | SCR_000597 | Ddbj Omics aRchive | 2026-08-05 10:43:12 | 0 | |||||
|
GONUTS Resource Report Resource Website 1+ mentions |
GONUTS (RRID:SCR_000653) | GONUTS | data or information resource, wiki, narrative resource, database | A wiki where users of the Gene Ontology can contribute and view notes about how specific GO terms are used. GONUTS can also be used as a GO term browser, or to search for GO annotations of specific genes from included organisms. The rationale for this wiki is based on helping new users of the gene ontology understand and use it. The GONUTS wiki is not an official product of the the Gene Ontology consortium. The GO consortium has a public wiki at their website, http://wiki.geneontology.org/. Maintaining the ontology involves many decisions to carefully choose terms and relationships. These decisions are currently made at GO meetings and via online discussion using the GO mailing lists and the Sourceforge curator request tracker. However, it is difficult for someone starting to use GO to understand these decisions. Some insight can be obtained by mining the tracker, the listservs and the minutes of GO meetings, but this is difficult, as these discussions are often dispersed and sometimes don't contain the GO accessions in the relevant messages. Wikis provide a way to create collaboratively written documentation for each GO term to explain how it should be used, how to satisfy the true path requirement, and whether an annotation should be placed at a different level. In addition, the wiki pages provide a discussion space, where users can post questions and discuss possible changes to the ontology. GONUTS is currently set up so anyone can view or search, but only registered users can edit or add pages. Currently registered users can create new users, and we are working to add at least one registered user for each participating database (So far we have registered users at EcoliHub, EcoCyc, GOA, BeeBase, SGD, dictyBase, FlyBase, WormBase, TAIR, Rat Genome Database, ZFIN, MGI, UCL and AgBase... | ontology or annotation browser, ontology or annotation search engine, ontology or annotation editor, protein |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: EcoliHub |
NIGMS 1U24 GM077905-01; NIGMS U24 GM088849 |
PMID:22110029 | Free for academic use, The community can contribute to this resource | OMICS_02268, nlx_30164 | SCR_000653 | Gene Ontology Normal Usage Tracking System, GONUTS wiki | 2026-08-05 10:43:12 | 1 | |||||
|
forqs Resource Report Resource Website |
forqs (RRID:SCR_000643) | forqs | software application, simulation software, software resource | Software for forward-in-time population genetics simulation that tracks individual haplotype chunks as they recombine each generation. It also also models quantitative traits and selection on those traits. | c++, linux, osx, windows, command line, simulation, recombination, quantitative trait, selection, haplotype pattern |
is listed by: OMICtools has parent organization: University of California at Los Angeles; California; USA has parent organization: Bitbucket |
NHGRI HG002536; NHGRI R01 HG007089; NSF EF-0928690 |
PMID:24336146 | Free, Available for download, Freely available | OMICS_02196 | SCR_000643 | Forward-in-time simulation of Recombination, and Selection, Quantitative traits | 2026-08-05 10:43:12 | 0 | |||||
|
Scaffold builder Resource Report Resource Website |
Scaffold builder (RRID:SCR_000556) | scaffold_builder | data analysis service, production service resource, service resource, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Tool designed to generate scaffolds (super contigs of sequences joined by N-bases) using the homology provided by a closely related reference sequence. Scaffold_builder is an advanced wrapper for Nucmer, written in Python that resolves several situations that may arise when mapping contigs to the reference genome. | scaffolding |
is listed by: OMICtools has parent organization: San Diego Supercomputer Center |
PMID:24267787 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00046 | SCR_000556 | 2026-08-05 10:43:11 | 0 | |||||||
|
AdaptiveCrawler Resource Report Resource Website |
AdaptiveCrawler (RRID:SCR_000573) | AdaptiveCrawler | software resource, web application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9,2022. A web crawler that can intelligently acquire social media content on the Internet to meet the specific online data source acquisition needs of cancer researchers. | web crawler, acquire social media content on Internet, cancer research, |
is listed by: OMICtools has parent organization: Oak Ridge National Laboratory |
Cancer, Breast cancer, Lung cancer | PMID:24078710 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01170 | SCR_000573 | Adaptive Crawler, Smart Web Crawler | 2026-08-05 10:43:11 | 0 | |||||
|
Skylign Resource Report Resource Website 10+ mentions |
Skylign (RRID:SCR_001176) | Skylign | software resource, data analysis service, production service resource, service resource, analysis service resource | A tool for creating logos representing both sequence alignments and profile hidden Markov models. The interactive logos enable scrolling, zooming, and inspection of underlying values. Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequences and by combining observed counts with informed priors. It also simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position. | sequence alignment, profile, logo, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Janelia Research |
PMID:24410852 | Creative Commons Attribution License, v3 Unported | biotools:skylign, OMICS_02182 | https://bio.tools/skylign | SCR_001176 | Skylign - Interactive logos for alignments and profile HMMs | 2026-08-05 10:43:19 | 13 | |||||
|
WiggleTools Resource Report Resource Website 1+ mentions |
WiggleTools (RRID:SCR_001170) | WiggleTools | data processing software, software library, software application, software toolkit, software resource | A multithreaded software library that computes statistics on large numbers of datasets, generating statistical summaries within minutes with limited memory requirements, whether on the whole genome or on selected regions. | visualization, statistical analysis, parallel processing, genome |
is listed by: OMICtools has parent organization: European Bioinformatics Institute |
PMID:24363377 | Apache License, v2 | OMICS_02188 | SCR_001170 | 2026-08-05 10:43:19 | 1 | |||||||
|
sim4cc Resource Report Resource Website |
sim4cc (RRID:SCR_001204) | data processing software, image analysis software, software application, alignment software, software resource | Software tool as cross species spliced alignment program.Heuristic sequence alignment tool for comparing cDNA sequence with genomic sequence containing homolog of gene in another species. | Cross species spliced alignment, unix, sequence alignment, cdna sequence, genomic sequence, homolog, gene, splice, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Johns Hopkins University; Maryland; USA |
NSF CLS20163A; Sloan Research Fellowship ; NLM R01 LM006845 |
PMID:19429899 | Free, Available for download, Freely available | biotools:sim4cc, OMICS_02145 | https://bio.tools/sim4cc | SCR_001204 | 2026-08-05 10:43:19 | 0 | ||||||
|
Omixon Target Data Analysis Resource Report Resource Website |
Omixon Target Data Analysis (RRID:SCR_001207) | Omixon Target | data processing software, software application, data analysis software, software toolkit, commercial organization, software resource | Software application suite to help clinical labs adopt next generation sequencing for the analysis of diagnostic gene targets. | next-generation sequencing, gene target, windows, linux, mac, gene, diagnostic |
is listed by: OMICtools is parent organization of: Omixon Target HLA Typing |
License required | OMICS_02141 | SCR_001207 | 2026-08-05 10:43:20 | 0 | ||||||||
|
bsseq Resource Report Resource Website 1+ mentions |
bsseq (RRID:SCR_001072) | data processing software, software application, sequence analysis software, data analysis software, software resource | R package with tools for analyzing and visualizing bisulfite sequencing data. | bisulfite sequencing, analyze, r, sequence analysis software, data analysis software, 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_01847, biotools:bsseq | https://bio.tools/bsseq | SCR_001072 | bsseq - Analyze manage and store bisulfite sequencing data | 2026-08-05 10:43:18 | 8 | |||||||
|
MmPalateMiRNA Resource Report Resource Website 1+ mentions |
MmPalateMiRNA (RRID:SCR_001070) | data processing software, source code, software application, data analysis software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software R package written for analysis of murine palate miRNA two-color expression data. | murine, palate, mirna, two color expression, open source, r |
is listed by: OMICtools is hosted by: Bioconductor |
PMID:23298515 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00788 | SCR_001070 | 2026-08-05 10:43:18 | 1 | ||||||||
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R453Plus1Toolbox Resource Report Resource Website 1+ mentions |
R453Plus1Toolbox (RRID:SCR_001105) | data processing software, software application, data analysis software, sequence analysis software, software toolkit, software resource | R software toolbox of functions for the analysis of data generated by Roche's 454 sequencing platform. Additional functions are included for quality assurance, annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. A pipeline for the detection of structural variants is provided. | genome, sequence, visualization, structural variants, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
PMID:21349869 | Free, Available for download, Freely available | OMICS_01354 | SCR_001105 | 2026-08-05 10:43:18 | 4 | ||||||||
|
RmiR Resource Report Resource Website |
RmiR (RRID:SCR_001069) | RmiR | data processing software, software application, sequence analysis software, data analysis software, software resource | R package that contains functions to merge microRNA and respective targets using different databases. | micro rna, mrna, function, target, r, sequence analysis software |
is listed by: OMICtools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00789 | https://rdrr.io/bioc/RmiR/ | SCR_001069 | 2026-08-05 10:43:17 | 0 | |||||||
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CGEN Resource Report Resource Website 10+ mentions |
CGEN (RRID:SCR_001251) | CGEN | software resource, data processing software, software application, data analysis software | Software R package for analysis of case-control studies in genetic epidemiology. | genetic, epidemiology, r, case-control, clustering, multiple comparison, snp |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21387464 | Free, Available for download, Freely available | OMICS_02089 | SCR_001251 | CGEN - An R package for analysis of case-control studies in genetic epidemiology | 2026-08-05 10:43:19 | 17 | ||||||
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SplitSeek Resource Report Resource Website 1+ mentions |
SplitSeek (RRID:SCR_001012) | data processing software, software application, sequence analysis software, data analysis software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented September 20, 2016. A program for de novo prediction of splice junctions in RNA-seq data. | bioinformatics alignment, sequence analysis software, de novo, prediction, rna seq, rna, splice junction, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20236510 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:splitseek, OMICS_01253 | https://bio.tools/splitseek | http://www.uppmax.uu.se/software/splitseek | SCR_001012 | 2026-08-05 10:43:17 | 1 | ||||||
|
Jmosaics Resource Report Resource Website |
Jmosaics (RRID:SCR_001094) | data processing software, software application, sequence analysis software, data analysis software, software resource | R software that detects enriched regions of ChIP-seq data sets jointly. | chip seq, data, genomics, sequencing, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
Free, Available for download, Freely available | OMICS_00445 | SCR_001094 | 2026-08-05 10:43:19 | 0 | |||||||||
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GDC Resource Report Resource Website 1+ mentions |
GDC (RRID:SCR_001007) | GDC | data processing software, data management software, software application, data analysis software, software resource | A C++ application designed for compression of genome collections from the same species. | compression, genome collection, c++, genome, software |
is listed by: OMICtools is hosted by: GitHub |
DOI:10.1038/srep11565 | Source code available for download | OMICS_00958 | https://github.com/refresh-bio/GDC2 | SCR_001007 | GDC 2, Genome Differential Compressor, Genome Differential Compressor (GDC) | 2026-08-05 10:43:17 | 1 |
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