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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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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AthaMap Resource Report Resource Website 50+ mentions |
AthaMap (RRID:SCR_006717) | data or information resource, database | Genome wide map of putative transcription factor binding sites in Arabidopsis thaliana genome.Data in AthaMap is based on published transcription factor (TF) binding specificities available as alignment matrices or experimentally determined single binding sites.Integrated transcriptional and post transcriptional data.Provides web tools for analysis and identification of co-regulated genes. Provides web tools for database assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana. | gene, arabidopsis thaliana, binding site, genome, transcription factor, small rna binding site, small rna, rna, microrna, cis-regulatory element, post-transcriptional regulation, FASEB list |
is listed by: OMICtools is listed by: bio.tools has parent organization: Technical University of Braunschweig; Braunschweig; Germany |
PMID:22800758 PMID:21177332 PMID:18842622 PMID:17148485 PMID:16922688 PMID:15980498 PMID:14681436 |
Free, Freely available | nif-0000-02583, biotools:athamap, OMICS_00549, nif-0000-20814, SCR_013106 | https://bio.tools/athamap | SCR_006717 | SciCrunch Registry | Arabidopsis thaliana Map | 2026-09-26 02:18:29 | 50 | ||||||
|
NCBI Epigenomics Resource Report Resource Website 10000+ mentions |
NCBI Epigenomics (RRID:SCR_006151) | Epigenomics | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022. | genome-wide map, dna, histone, modification, epigenomic, genome, gold standard, gene mapping, gene amplification, genetic code, gene library, dna fingerprinting, chromatin, histone modification, dna methylation, dnaase footprinting, genome wide association study, gene expression |
is listed by: re3data.org is listed by: OMICtools is related to: Roadmap Epigenomics Project has parent organization: NCBI |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151643, OMICS_01848, r3d100010782 | https://doi.org/10.17616/R34K7J | http://www.ncbi.nlm.nih.gov/epigenomics | SCR_006151 | SciCrunch Registry | NCBI Epigenomic Gateway, National Center for Biotechnology Information Epigenomics, NCBI Epigenomic Hub | 2026-09-26 02:18:30 | 14631 | |||||
|
GBrowse Resource Report Resource Website 10+ mentions |
GBrowse (RRID:SCR_006829) | GBrowse | data or information resource, database | A database and interactive web site for manipulating and displaying annotations on genomes. Features include: detailed views of the genome; use of a variety of premade or personally made glyphs ; customizable order and appearance of tracks by administrators and end-users; search by annotation ID, name, or comment; support of third party annotation using GFF formats; DNA and GFF dumps; connectivity to different databases, including BioSQL and Chado; and a customizable plug-in architecture (e.g. run BLAST, find oligonucleotides, design primers, etc.). GBrowse is distributed as source code for Macintosh OS X, UNIX and Linux platforms, and as pre-packaged binaries for Windows machines. It can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed. The wiki portion accepts data submissions. | genome, annotation, database, perl, virus, dna, protein, reference sequence, chromosome, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: WormBase is related to: FlyBase is related to: International HapMap Project has parent organization: Generic Model Organism Database Project has parent organization: Indiana University; Indiana; USA |
Howard Hughes Medical Institute ; NHGRI HG00739; NHGRI P41HG02223 |
PMID:19957275 PMID:18428797 PMID:12368253 PMID:21400697 PMID:20194461 PMID:19357095 DOI:10.1002/0471250953.bi0909s28 |
The community can contribute to this resource, Requires Perl 5.8.6 or higher and the Apache web server | OMICS_00910, biotools:gbrowse, nif-0000-30597 | http://gmod.org/wiki/GBrowse, https://bio.tools/gbrowse, https://sources.debian.org/src/gbrowse/ | SCR_006829 | SciCrunch Registry | Generic Genome Browser | 2026-09-26 02:18:30 | 43 | ||||
|
Next-Gen Sequencing Resource Report Resource Website |
Next-Gen Sequencing (RRID:SCR_007245) | Next-Gen Sequencing | blog, data or information resource, narrative resource | A working guide to the rapidly developing world of Next-Generation DNA sequencing, with an emphasis on bioinformatics. | is listed by: OMICtools | OMICS_01717 | SCR_007245 | SciCrunch Registry | 2026-09-26 02:18:32 | 0 | ||||||||||
|
Search Tool for Interactions of Chemicals Resource Report Resource Website 1000+ mentions |
Search Tool for Interactions of Chemicals (RRID:SCR_007947) | STITCH | data or information resource, database | Database to explore known and predicted interactions of chemicals and proteins. It integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug-target relationships. Inferred information from phenotypic effects, text mining and chemical structure similarity is used to predict relations between chemicals. STITCH further allows exploring the network of chemical relations, also in the context of associated binding proteins. Each proposed interaction can be traced back to the original data sources. The database contains interaction information for over 68,000 different chemicals, including 2200 drugs, and connects them to 1.5 million genes across 373 genomes and their interactions contained in the STRING database. | drug-target relationship, chemical, chemical-protein interaction, chemical relationship, crystal structure, metabolic pathway interaction, protein, interaction, small molecule, drug, interaction network, FASEB list |
is listed by: OMICtools is related to: Integrated Molecular Interaction Database has parent organization: European Molecular Biology Laboratory |
BMBF ; European Union FP6 EMBO ; ProBioC |
PMID:22075997 PMID:19897548 PMID:18084021 |
r3d100012165, OMICS_01589, nif-0000-03499 | https://doi.org/10.17616/R3606X, https://doi.org/10.17616/R3606X | SCR_007947 | SciCrunch Registry | STITCH: Chemical-Protein Interactions | 2026-09-26 02:18:39 | 1054 | |||||
|
miRGator Resource Report Resource Website 50+ mentions |
miRGator (RRID:SCR_007793) | miRGator | data or information resource, database | Database of compiled, public, deep sequencing miRNA data and several novel tools to facilitate exploration of massive data. The miR-seq browser supports users to examine short read alignment with the secondary structure and read count information available in concurrent windows. Features such as sequence editing, sorting, ordering, import and export of user data are of great utility for studying iso-miRs, miRNA editing and modifications. miRNA����??target relation is essential for understanding miRNA function. Coexpression analysis of miRNA and target mRNAs, based on miRNA-seq and RNA-seq data from the same sample, is visualized in the heat-map and network views where users can investigate the inverse correlation of gene expression and target relations, compiled from various databases of predicted and validated targets. | genome, functional annotation, microrna, expression profile, mir-seq, mirna-mrna target relation, expression correlation, FASEB list |
is listed by: OMICtools has parent organization: Korea Research Institute of Bioscience and Biotechnology; Daejeon; South Korea |
Korean Rural Development Administration 20070401034010; Korean Ministry of Science and Technology ; Ministry of Education and Human Resources Development |
PMID:23193297 PMID:21062822 PMID:17942429 |
nif-0000-03136, OMICS_00363 | http://203.255.191.19/MEXWebApp/, http://genome.ewha.ac.kr/miRGator/miRGator.html | SCR_007793 | SciCrunch Registry | miRGator: an integrated system for functional annotation of microRNAs | 2026-09-26 02:18:36 | 55 | |||||
|
Transterm Resource Report Resource Website 10+ mentions |
Transterm (RRID:SCR_008244) | data or information resource, database | Database that provides access to mRNA sequences and associated regulatory elements that were processed from Genbank. These mRNA sequences include complete genomes, which are divided into 5-prime UTRs, 3-prime UTRs, initiation sequences, termination regions and full CDS sequences. This data can be searched for a range of properties including specific mRNA sequences, mRNA motifs, codon usage, RSCU values, information content, etc. | element, gene, 3' utr, 5' utr, codon, genome, genomic, initiation, motif, mrna, nucleotide sequences, transcriptional regulator sites, transcription factors databases, region, regulatory, rna sequence, species, termination |
is listed by: Debian is listed by: OMICtools has parent organization: University of Otago; Dunedin; New Zealand |
DOI:10.1186/gb-2007-8-2-r22 | Public | nif-0000-21399, OMICS_06165 | https://sources.debian.org/src/transtermhp/ | http://uther.otago.ac.nz/Transterm.html | SCR_008244 | SciCrunch Registry | 2026-09-26 02:18:41 | 17 | ||||||
|
OMICS! OMICS! Resource Report Resource Website |
OMICS! OMICS! (RRID:SCR_008533) | OMICS! OMICS! | blog, data or information resource, narrative resource | A computational biologist''s personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery. | is listed by: OMICtools | OMICS_01719 | SCR_008533 | SciCrunch Registry | 2026-09-26 02:18:42 | 0 | ||||||||||
|
Exon Array Analyzer Resource Report Resource Website 1+ mentions |
Exon Array Analyzer (RRID:SCR_008684) | Exon Array Analyzer | analysis service resource, data analysis service, production service resource, service resource | Service that allows you to process CEL files from Affymetrix, Inc. GeneChip Exon 1.0 ST Arrays to identify alternative splicing. | is listed by: OMICtools | OMICS_00754 | SCR_008684 | SciCrunch Registry | 2026-09-26 02:18:43 | 4 | ||||||||||
|
SNPs3D Resource Report Resource Website 100+ mentions |
SNPs3D (RRID:SCR_010787) | SNPs3D | data or information resource, database | 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 | SciCrunch Registry | 2026-09-26 02:18:47 | 117 | |||||||
|
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 | SciCrunch Registry | 2026-09-26 02:18:47 | 12 | ||||||||||
|
Omixon blog Resource Report Resource Website |
Omixon blog (RRID:SCR_010020) | Omixon blog | blog, data or information resource, 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 | SciCrunch Registry | 2026-09-26 02:18:44 | 0 | ||||||||||
|
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 | SciCrunch Registry | The Genomic HyperBrowser | 2026-09-26 02:18:47 | 20 | |||||||
|
UCSC Cancer Genomics Browser Resource Report Resource Website 500+ mentions |
UCSC Cancer Genomics Browser (RRID:SCR_011796) | Cancer Genomics Browser | data or information resource, database, service resource | A suite of web-based tools to visualize, integrate and analyze cancer genomics and its associated clinical data. It is possible to display your own clinical data within one of their datasets. | genome, genomics, clinical, next-generation sequencing, chromosome, gene, FASEB list |
is listed by: OMICtools has parent organization: University of California at Santa Cruz; California; USA |
Cancer | NCI ; NHGRI ; American Association for Cancer Research ; UCSF Comprehensive Cancer Center ; California Institute for Quantitative Biosciences |
PMID:23109555 PMID:21059681 PMID:19333237 |
Acknowledgement requested | OMICS_00925 | SCR_011796 | SciCrunch Registry | 2026-09-26 02:18:47 | 589 | |||||
|
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 | SciCrunch Registry | 2026-09-26 02:18:44 | 23 | ||||||||
|
TarBase Resource Report Resource Website 500+ mentions |
TarBase (RRID:SCR_010841) | DIANA-TarBase | data or information resource, database, 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 | SciCrunch Registry | DIANA-TarBase v7.0, DIANA-TarBase v.8, DIANA-TarBase v.6 | 2026-09-26 02:18:47 | 869 | ||||
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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 | SciCrunch Registry | 2026-09-26 02:18:47 | 14 | |||||||
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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 | SciCrunch Registry | 2026-09-26 02:18:47 | 93 | |||||||||
|
PlanTAPDB Resource Report Resource Website |
PlanTAPDB (RRID:SCR_010897) | PlanTAPDB | data or information resource, database | A phylogeny-based comprehensive database of plant transcription associated proteins. | is listed by: OMICtools | PMID:17337525 | Free | OMICS_00558 | SCR_010897 | SciCrunch Registry | 2026-09-26 02:18:47 | 0 | ||||||||
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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 | SciCrunch Registry | 2026-09-26 02:18:47 | 4781 |
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