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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Omixon blog Resource Report Resource Website |
Omixon blog (RRID:SCR_010020) | Omixon blog | data or information resource, blog, narrative resource | We share commentaries, news and announcement that advance our goal of helping clinical labs to adopt next generation sequencing for the analysis of diagnostic gene targets. | is listed by: OMICtools | OMICS_01720 | SCR_010020 | 2026-08-08 12:04:17 | 0 | ||||||||||
|
CPSS Resource Report Resource Website 10+ mentions |
CPSS (RRID:SCR_009395) | CPSS | analysis service resource, data analysis service, production service resource, service resource | Computational Platform for analysis of Small RNA deep Sequencing data BioStaCs group., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | is listed by: OMICtools | PMID:22576177 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00355 | SCR_009395 | 2026-08-08 12:04:24 | 23 | ||||||||
|
TarBase Resource Report Resource Website 500+ mentions |
TarBase (RRID:SCR_010841) | DIANA-TarBase | database, data or information resource, service resource | Manually curated database of experimentally supported animal microRNA targets. Collection of experimentally supported miRNA gene interactions. | mirna-gene interaction |
is listed by: OMICtools is provided by: DIANA Tools |
Fondation Santé Grant ; General Secretariat of Research and Technology ; Greece Grant ; Hellenic Foundation for Research and Innovation ; IKY Foundation |
PMID:22135297 PMID:29156006 |
Restricted | OMICS_00397 | http://carolina.imis.athena-innovation.gr/diana_tools/web/index.php?r=tarbasev8%2Findex/ | SCR_010841 | DIANA-TarBase v7.0, DIANA-TarBase v.8, DIANA-TarBase v.6 | 2026-08-08 12:04:21 | 869 | ||||
|
SNPs3D Resource Report Resource Website 100+ mentions |
SNPs3D (RRID:SCR_010787) | SNPs3D | database, data or information resource | A website which assigns molecular functional effects of non-synonymous SNPs based on structure and sequence analysis. | single nucleotide polymorphism, single nucleotide variation, gene, FASEB list |
is listed by: OMICtools has parent organization: University of Maryland; Maryland; USA |
NLM | The community can contribute to this resource | OMICS_00163 | SCR_010787 | 2026-08-08 12:04:27 | 117 | |||||||
|
omiRas Resource Report Resource Website 10+ mentions |
omiRas (RRID:SCR_010833) | omiRas | analysis service resource, data analysis service, production service resource, service resource | A web server for the annotation, comparison and visualization of interaction networks of non-coding RNAs derived from small RNA-Sequencing experiments of two different conditions. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23946503 | biotools:omiras, OMICS_00383 | https://bio.tools/omiras | SCR_010833 | 2026-08-08 12:04:27 | 14 | |||||||
|
CGHweb Resource Report Resource Website 10+ mentions |
CGHweb (RRID:SCR_010923) | CGHweb | analysis service resource, data analysis service, production service resource, service resource | Data analysis service enabling users to analyse their array-CGH data with multiple algorithms simultaneously. |
is listed by: OMICtools has parent organization: Harvard Medical School; Massachusetts; USA |
OMICS_00713 | SCR_010923 | 2026-08-08 12:04:27 | 12 | ||||||||||
|
Align-GVGD Resource Report Resource Website 50+ mentions |
Align-GVGD (RRID:SCR_010772) | Align-GVGD | analysis service resource, data analysis service, production service resource, service resource | A freely available, web-based program that combines the biophysical characteristics of amino acids and protein multiple sequence alignments to predict where missense substitutions in genes of interest fall in a spectrum from enriched delterious to enriched neutral. | is listed by: OMICtools | Free | OMICS_00125 | SCR_010772 | 2026-08-08 12:04:28 | 93 | |||||||||
|
PlanTAPDB Resource Report Resource Website |
PlanTAPDB (RRID:SCR_010897) | PlanTAPDB | database, data or information resource | A phylogeny-based comprehensive database of plant transcription associated proteins. | is listed by: OMICtools | PMID:17337525 | Free | OMICS_00558 | SCR_010897 | 2026-08-08 12:04:28 | 0 | ||||||||
|
MutationTaster Resource Report Resource Website 1000+ mentions |
MutationTaster (RRID:SCR_010777) | MutationTaster | analysis service resource, data analysis service, production service resource, service resource | Evaluates disease-causing potential of sequence alterations. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
PMID:20676075 | Acknowledgement requested | biotools:mutation_taster, OMICS_00153 | https://bio.tools/mutation_taster | SCR_010777 | 2026-08-08 12:04:21 | 4781 | ||||||
|
Genomic HyperBrowser Resource Report Resource Website 10+ mentions |
Genomic HyperBrowser (RRID:SCR_010909) | Genomic HyperBrowser | analysis service resource, data analysis service, production service resource, service resource | A generic web-based system, providing statistical methodology and computing power to handle a variety of biological inquires on genomic datasets. | genomic, genomic track, gene regulation, disease association, epigenetic modification, genome |
is listed by: OMICtools has parent organization: University of Oslo; Oslo; Norway |
PMID:23632163 PMID:21182759 |
OMICS_00638 | SCR_010909 | The Genomic HyperBrowser | 2026-08-08 12:04:29 | 20 | |||||||
|
WU-BLAST Resource Report Resource Website 100+ mentions |
WU-BLAST (RRID:SCR_011824) | WU-BLAST | analysis service resource, data analysis service, production service resource, service resource | Tool to find regions of sequence similarity within selected protein databases quickly, with minimum loss of sensitivity. | protein, dna, rna |
is listed by: OMICtools is listed by: SoftCite has parent organization: European Bioinformatics Institute |
OMICS_01001 | SCR_011824 | 2026-08-08 12:04:28 | 135 | |||||||||
|
CancerResource Resource Report Resource Website 1+ mentions |
CancerResource (RRID:SCR_011945) | database, data or information resource | Comprehensive database of cancer relevant proteins and compound interactions supported by experimental knowledge.Knowledgebase for drug-target relationships related to cancer as well as for supporting information or experimental data. | compound, drug, target gene, cancer relevant proteins, compound interactions, drug-target relationships, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Cancer | International Research Training Group IRTG ; DFG ; Federal Ministry of Education and Research BMBF ; European Union |
PMID:20952398 | Free, Freely available | biotools:cancerresource, OMICS_01576 | https://bio.tools/cancerresource | http://bioinf-data.charite.de/cancerresource/index.php?site=home | SCR_011945 | 2026-08-08 12:04:28 | 5 | ||||
|
Blue Collar Bioinformatics Resource Report Resource Website 1+ mentions |
Blue Collar Bioinformatics (RRID:SCR_012913) | Blue Collar Bioinformatics | data or information resource, blog, narrative resource | This blog will appeal to those dealing with the practical day to day work of biological data analysis and presentation. | is listed by: OMICtools | OMICS_01712 | SCR_012913 | 2026-08-08 12:04:31 | 1 | ||||||||||
|
ComiR Resource Report Resource Website 10+ mentions |
ComiR (RRID:SCR_013023) | ComiR | analysis service resource, data analysis service, production service resource, service resource | Data analysis service that predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms: miRanda, PITA, TargetScan and mirSVR. The composite scores of the four algorithms are then combined using a support vector machine trained on Drosophila Ago1 IP data. | mirna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Pittsburgh; Pennsylvania; USA |
NLM ; Fondazione RiMED |
PMID:23703208 PMID:23284279 |
Acknowledgement requested | OMICS_00395, biotools:comir | https://bio.tools/comir | SCR_013023 | Combinatorial miRNA targeting, ComiR: Combinatorial miRNA target prediction tool, ComiR - Combinatorial miRNA target prediction tool | 2026-08-08 12:04:31 | 26 | ||||
|
CoMet Resource Report Resource Website 500+ mentions |
CoMet (RRID:SCR_011925) | CoMet | analysis service resource, data analysis service, production service resource, service resource | A web-server for fast comparative functional profiling of metagenomes. | is listed by: OMICtools | OMICS_01477 | SCR_011925 | CoMet - a web-server for fast comparative functional profiling of metagenomes | 2026-08-08 12:04:28 | 991 | |||||||||
|
PhyloPythiaS Resource Report Resource Website 10+ mentions |
PhyloPythiaS (RRID:SCR_011923) | PPS | analysis service resource, data analysis service, production service resource, service resource | Web Server for Taxonomic Assignment of Metagenome Sequences that is a fast and accurate sequence composition-based classifier that utilizes the hierarchical relationships between clades. Taxonomic assignments with the web server can be made with a generic model, or with sample-specific models that users can specify and create. Several interactive visualization modes and multiple download formats allow quick and convenient analysis and downstream processing of taxonomic assignments. | metagenome, sequence, taxonomy, classification | is listed by: OMICtools | PMID:22745671 PMID:21358620 |
OMICS_01460 | http://phylopythias.cs.uni-duesseldorf.de/index.php?phase=wait | SCR_011923 | 2026-08-08 12:04:22 | 12 | |||||||
|
University of Pittsburgh, Health Sciences Library System Resource Report Resource Website 10+ mentions |
University of Pittsburgh, Health Sciences Library System (RRID:SCR_011975) | HSLS | database, data or information resource | Database access to information services, educational opportunities, and resources in print and electronic format to faculty, students, and researchers in the schools of the health sciences. | journal, book, video |
is listed by: OMICtools has parent organization: University of Pittsburgh; Pennsylvania; USA |
PMID:17108360 | SCR_011975 | Pitt Health Sciences Library System, Pitt HSLS, Health Sciences Library System | 2026-08-08 12:04:28 | 10 | ||||||||
|
OMA Browser Resource Report Resource Website 10+ mentions |
OMA Browser (RRID:SCR_011978) | OMA | database, data or information resource | A database that identifies orthologs among publicly available, complete genomes. It offers a comprehensive search and numerous display options for 4.7 million proteins from 1000 species. The main features are the orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. | protein |
is listed by: OMICtools is related to: GermOnline has parent organization: ETH Zurich; Zurich; Switzerland |
PMID:21113020 PMID:17545180 |
Creative Commons Attribution-ShareAlike License, 2.5 | OMICS_01690 | SCR_011978 | Orthologous MAtrix | 2026-08-08 12:04:28 | 10 | ||||||
|
gsGator Resource Report Resource Website |
gsGator (RRID:SCR_012035) | gsGator | analysis service resource, data analysis service, production service resource, service resource | A web-based platform for functional interpretation of gene sets with features such as cross-species Gene Set Analysis (GSA), Flexible and Interactive GSA, simultaneous GSA for multiple gene set, and and a fully integrated network viewer for both visualizing GSA results and molecular networks. | linux, windows, gene, orthology, pathway, phenotype, mirna target, molecular network, genomic annotation, function |
is listed by: OMICtools is related to: Gene Ontology has parent organization: Ewha Womans University; Seoul; South Korea |
PMID:24423189 | Free, Public | OMICS_02233 | SCR_012035 | 2026-08-08 12:04:29 | 0 | |||||||
|
OrthoDB Resource Report Resource Website 1000+ mentions |
OrthoDB (RRID:SCR_011980) | database, data or information resource | Database of orthologous protein coding genes across vertebrates, arthropods, fungi, basal metazoans, and bacteria. | Hierarchical catalog, ortholog, protein coding genes, mapping genomics to functional data, FASEB list |
is listed by: OMICtools has parent organization: University of Geneva; Geneva; Switzerland |
Swiss National Foundation | PMID:23180791 | Free, Freely available | OMICS_01692 | http://cegg.unige.ch/orthodb7 | SCR_011980 | OrthoDB: Database of Orthologous Groups, OrthoDB v7, OrthoDB - The Hierarchical Catalog of Orthologs, OrthoDB v10 | 2026-08-08 12:04:22 | 1143 |
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