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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ENA Sequence Search Resource Report Resource Website 1+ mentions |
ENA Sequence Search (RRID:SCR_013170) | ENA Sequence Search | analysis service resource, data analysis service, production service resource, service resource | A nucleotide sequence similiary search tool which is far faster than BLAST for large datasets, with only a marginal loss in search sensitivity. | nucleotide sequencing |
is listed by: OMICtools has parent organization: European Nucleotide Archive (ENA) |
OMICS_00993 | SCR_013170 | SciCrunch Registry | 2026-09-26 02:18:50 | 7 | |||||||||
|
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 | SciCrunch Registry | Combinatorial miRNA targeting, ComiR: Combinatorial miRNA target prediction tool, ComiR - Combinatorial miRNA target prediction tool | 2026-09-26 02:18:49 | 26 | ||||
|
CRAVAT Resource Report Resource Website 10+ mentions |
CRAVAT (RRID:SCR_012776) | CRAVAT | analysis service resource, data analysis service, production service resource, service resource | A web-based application designed with an easy-to-use interface to facilitate the high-throughput assessment and prioritization of genes and missense alterations important for cancer tumorigenesis. |
is listed by: OMICtools has parent organization: Johns Hopkins University; Maryland; USA |
Cancer | NCI CA 152432; NSF DBI 0845275; NCI 1U01CA180956-01 |
OMICS_00147 | SCR_012776 | SciCrunch Registry | cancer-related analysis of variants toolkit | 2026-09-26 02:18:48 | 30 | |||||||
|
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 | SciCrunch Registry | 2026-09-26 02:18:47 | 135 | |||||||||
|
CancerResource Resource Report Resource Website 1+ mentions |
CancerResource (RRID:SCR_011945) | data or information resource, database | 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 | DFG ; European Union ; Federal Ministry of Education and Research BMBF ; International Research Training Group IRTG |
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 | SciCrunch Registry | 2026-09-26 02:18:47 | 5 | ||||
|
Blue Collar Bioinformatics Resource Report Resource Website 1+ mentions |
Blue Collar Bioinformatics (RRID:SCR_012913) | Blue Collar Bioinformatics | blog, data or information resource, 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 | SciCrunch Registry | 2026-09-26 02:18:49 | 1 | ||||||||||
|
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 | SciCrunch Registry | CoMet - a web-server for fast comparative functional profiling of metagenomes | 2026-09-26 02:18:47 | 991 | |||||||||
|
Human Transcriptome Database for Alternative Splicing Resource Report Resource Website |
Human Transcriptome Database for Alternative Splicing (RRID:SCR_013305) | H-DBAS | data or information resource, database | A specialized database for human alternative splicing (AS) based on H-Invitational full-length cDNAs. H-DBAS offers unique data and viewer for human Alternative Splicing (AS) analysis. It contains: * Genome-wide representative alternative splicing variants (RASVs) identified from following datasets * H-Inv full-length cDNAs (resource summary): H-Invitational cDNA dataset * H-Inv all transcripts (resource summary): Published human mRNA dataset * Mouse full-length cDNAs (resource summary): Mouse cDNA dataset * RASVs affecting protein functions such as protein motif, GO, subcellular localization signal and transmembrane domain * Conserved RASVs compared with mouse genome and the full-length cDNAs (H-Inv full-length cDNAs only) | alternative splicing, alternative splicing variant, cdna, transcriptome, h-invitational, rna-seq, rna, comparative genomics |
is listed by: OMICtools has parent organization: National Institute of Advanced Industrial Science and Technology |
PMID:19969536 PMID:17130147 |
nif-0000-02935, OMICS_01887 | SCR_013305 | SciCrunch Registry | H-DBAS - Human-transcriptome DataBase for Alternative Splicing | 2026-09-26 02:18:50 | 0 | |||||||
|
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 | SciCrunch Registry | 2026-09-26 02:18:47 | 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 | data or information resource, database | 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 | SciCrunch Registry | Pitt Health Sciences Library System, Pitt HSLS, Health Sciences Library System | 2026-09-26 02:18:48 | 10 | ||||||||
|
OMA Browser Resource Report Resource Website 10+ mentions |
OMA Browser (RRID:SCR_011978) | OMA | data or information resource, database | 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 | SciCrunch Registry | Orthologous MAtrix | 2026-09-26 02:18:48 | 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 | SciCrunch Registry | 2026-09-26 02:18:48 | 0 | |||||||
|
OrthoDB Resource Report Resource Website 1000+ mentions |
OrthoDB (RRID:SCR_011980) | data or information resource, database | 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 | SciCrunch Registry | OrthoDB: Database of Orthologous Groups, OrthoDB v7, OrthoDB - The Hierarchical Catalog of Orthologs, OrthoDB v10 | 2026-09-26 02:18:48 | 1143 | |||||
|
CoreGenomics Resource Report Resource Website |
CoreGenomics (RRID:SCR_011985) | CoreGenomics | blog, data or information resource, narrative resource | This blog focusses on next-generation sequencing and microarray technologies. | is listed by: OMICtools | OMICS_01713 | SCR_011985 | SciCrunch Registry | 2026-09-26 02:18:48 | 0 | ||||||||||
|
Bio-IT World Resource Report Resource Website 1+ mentions |
Bio-IT World (RRID:SCR_011986) | Bio-IT World | blog, data or information resource, narrative resource | A leading source of news on technology and innovation in life sciences IT, informatics, genomics, next-gen, drug discovery, development, and clinical trials. | informatics, computer science, biomedical research, drug discovery, information technology, next-generation technology, big data, personalized medicine | is listed by: OMICtools | OMICS_01727 | SCR_011986 | SciCrunch Registry | Bio-ITWorld.com, Bio-ITWorld | 2026-09-26 02:18:48 | 3 | ||||||||
|
WebMGA Resource Report Resource Website 100+ mentions |
WebMGA (RRID:SCR_011951) | WebMGA | analysis service resource, data analysis service, production service resource, service resource | A customizable web server for fast metagenomic analysis. |
is listed by: OMICtools has parent organization: University of California at San Diego; California; USA |
OMICS_01524 | SCR_011951 | SciCrunch Registry | 2026-09-26 02:18:47 | 196 | ||||||||||
|
NGS Expert Blog Resource Report Resource Website |
NGS Expert Blog (RRID:SCR_013218) | NGS Expert Blog | blog, data or information resource, narrative resource | Blog including established profound know-how and proprietary protocols to cover a broad range of applications. | next generation sequencing | is listed by: OMICtools | OMICS_01718 | SCR_013218 | SciCrunch Registry | 2026-09-26 02:18:50 | 0 | |||||||||
|
GenoREAD Resource Report Resource Website |
GenoREAD (RRID:SCR_012007) | GenoREAD | analysis service resource, data analysis service, production service resource, service resource | A sequence verification pipeline where users can submit trace files to verify if a clone''s physical sequence matches its reference sequence. | clone, verification, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Virginia Bioinformatics Institute |
PMID:23042248 | Acknowledgement requested | OMICS_01823, biotools:genoread | https://bio.tools/genoread | SCR_012007 | SciCrunch Registry | GenoREAD - Sequencing Verification Pipeline | 2026-09-26 02:18:48 | 0 | |||||
|
Genomics of Drug Sensitivity in Cancer Resource Report Resource Website 1000+ mentions |
Genomics of Drug Sensitivity in Cancer (RRID:SCR_011956) | Genomics of Drug Sensitivity in Cancer | data or information resource, database | A genomics database project is an academic research program to identify molecular features of cancers that predict response to anti-cancer drugs. | compound, gene, molecule, drug, FASEB list |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Cancer | Wellcome Trust | OMICS_01581 | SCR_011956 | SciCrunch Registry | 2026-09-26 02:18:47 | 2388 | |||||||
|
My Biomedical Informatics Blog Resource Report Resource Website |
My Biomedical Informatics Blog (RRID:SCR_012011) | My Biomedical Informatics Blog | blog, data or information resource, narrative resource | A blog about genetics, genomics, and medical research. | is listed by: OMICtools | OMICS_01832 | SCR_012011 | SciCrunch Registry | 2026-09-26 02:18:48 | 0 |
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