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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-02-14 02:06:14 | 116 | |||||||
|
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 | 2026-02-14 02:06:14 | 0 | ||||||||
|
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 | 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 | 2026-02-14 02:06:15 | 5 | ||||
|
University of Pittsburgh, Health Sciences Library System Resource Report Resource Website 1+ 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 | Pitt Health Sciences Library System, Pitt HSLS, Health Sciences Library System | 2026-02-14 02:06:47 | 7 | ||||||||
|
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 | Orthologous MAtrix | 2026-02-14 02:06:15 | 10 | ||||||
|
OrthoDB Resource Report Resource Website 500+ 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 | OrthoDB: Database of Orthologous Groups, OrthoDB v7, OrthoDB - The Hierarchical Catalog of Orthologs, OrthoDB v10 | 2026-02-14 02:06:40 | 999 | |||||
|
GLAD Resource Report Resource Website 100+ mentions |
GLAD (RRID:SCR_001284) | GLAD | software resource | Software for analysis of array CGH data: detection of breakpoints in genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified. | comparative genomic hybridization, breakpoint, copy number variation, microarray |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:15381628 | Free, Available for download, Freely available | OMICS_02053 | SCR_001284 | GLAD - Gain and Loss Analysis of DNA, Gain and Loss Analysis of DNA | 2026-02-14 02:05:06 | 283 | ||||||
|
Bycom Resource Report Resource Website |
Bycom (RRID:SCR_000659) | software resource | A software which can perform methylcytosine calling from BS-seq (WGBS and RRBS), and permits either unmapped reads (FASTQ) or mapped reads (SAM/BAM) to be used as the input data. Certain SNPs (C>A/G) can also be selected in the output. | methylcytosine, bs-seq, fastq, sam, bam, snps, snp, wgbs, rrbs, sorftw |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25255082 | Free, Available for download, Freely available | OMICS_00594 | SCR_000659 | 2026-02-14 02:04:50 | 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 | 2026-02-14 02:06:20 | 1418 | |||||||
|
Cancer Methylome System Resource Report Resource Website 1+ mentions |
Cancer Methylome System (RRID:SCR_012013) | CMS | data or information resource, database | Datbase and web-based system for visualization and analysis of genome-wide methylation data of human cancers. | gene, methylation, visualization |
is listed by: OMICtools has parent organization: University of Texas Health Science Center at San Antonio; Texas; USA |
Cancer, Normal | NCI | PMID:22035855 | Acknowledgement requested | OMICS_01836 | SCR_012013 | 2026-02-14 02:06:21 | 8 | |||||
|
Histone Systematic Mutation Database Resource Report Resource Website |
Histone Systematic Mutation Database (RRID:SCR_012015) | HistoneHits | data or information resource, database | A database for histone mutations and their phenotypes. | is listed by: OMICtools | PMID:19218532 | OMICS_01839 | SCR_012015 | 2026-02-14 02:06:15 | 0 | |||||||||
|
DBCAT Resource Report Resource Website 10+ mentions |
DBCAT (RRID:SCR_012014) | DBCAT | data or information resource, database | A database of CpG islands and analytical tools for identifying comprehensive methylation profiles in cancer cells. | is listed by: OMICtools | Cancer | PMID:21214365 | OMICS_01837 | SCR_012014 | 2026-02-14 02:06:47 | 40 | ||||||||
|
APPRIS Resource Report Resource Website 50+ mentions |
APPRIS (RRID:SCR_012019) | APPRIS | data or information resource, database | A database that houses annotations of human splice isoforms. It adds reliable protein structural and functional data and information from cross-species conservation. A visual representation of the annotations for each gene allows users to easily identify functional changes brought about by splicing events. In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, it also selects a single reference sequence for each gene, termed the principal isoform, based on the annotations of structure, function and conservation for each transcript. | isoform, function, annotation, splice, reference sequence, structure, conservation, transcript, FASEB list |
is listed by: OMICtools has parent organization: Spanish National Cancer Research Center |
PMID:23161672 | Free | OMICS_01881 | SCR_012019 | APPRIS - A system for annotating alternative splice isoforms | 2026-02-14 02:06:21 | 85 | ||||||
|
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 | H-DBAS - Human-transcriptome DataBase for Alternative Splicing | 2026-02-14 02:06:24 | 0 | |||||||
|
Monoclonal Antibody Index Resource Report Resource Website |
Monoclonal Antibody Index (RRID:SCR_013227) | MAI | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented September 13, 2016. A searchable biotechnology database e-books with information on more than 9000 monoclonal antibodies. This database has antibodies produced for the diagnosis and therapy of human cancer, Alzheimer's disease, AIDS, and other diseases as well as for biomarker and proteomics research. Information such as antibody name, species, type, characteristics, antigen characteristics, and developer or distributor of antibody as well as mentions in journals, patents, abstracts and reports up until 2012 are included. | antibody, monoclonal antibody, cancer, aids, sars, heart disease, vascular disease, coagulation disease, transplantation, inflammation, alzheimer's disease, autoimmunity, biomarker, proteomics, resource, research, database | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01773 | SCR_013227 | 2026-02-14 02:06:23 | 0 | ||||||||
|
Drosophila melanogaster Exon Database Resource Report Resource Website 1+ mentions |
Drosophila melanogaster Exon Database (RRID:SCR_013441) | DEDB | data or information resource, database | Database on Drosophila melanogaster exons presented in a splicing graph form. Data is based on release 3.2 of the Drosophila melanogaster genome annotations available at FlyBase. The gene structure information extracted from the annotations were checked, clustered and transformed into splicing graph. The splicing graph form of the gene constructs were then used for classification of the various types of alternative splicing events. In addition, Pfam domains were mapped onto the gene structure. Users can query the database using the query page using BLAST, FlyBase Gene Name, FlyBase Gene Symbol, Pfam Accession Number and Pfam Identifier. This allows users to determine the Drosophila melanogaster homology of their gene using a BLAST search and to visualize the alternative splicing variants if any. Users can also determine genes containing a particular domain using the Pfam Accession Numbers and Identifiers. | exon, gene, alternative splicing, annotation, classification, cluster, domain, genome, graph, homology, protein, splicing, structure, transcript, visualize, blast |
is listed by: OMICtools is related to: FlyBase has parent organization: National University of Singapore; Singapore; Singapore |
Agency for Science Technology and Research | PMID:15581431 | nif-0000-21118, OMICS_01894 | SCR_013441 | DEDB - Drosophila melanogaster Exon Database, DEDB : Drosophila melanogaster Exon Database | 2026-02-14 02:06:50 | 2 | ||||||
|
RARTF Resource Report Resource Website 1+ mentions |
RARTF (RRID:SCR_013457) | RARTF | data or information resource, database | Database of complete sets of Arabidopsis transcription factors with a variety of information on Arabidopsis thaliana transcription factor families including: full-length cDNA sequences, Ds-tagged mutants, multiple sequences alignments of family members, phylogenic trees, functional motifs, and so on. In addition, expression profiles of all transcription factor genes are available. | transcription factor, protein, gene, microarray, expression profile |
is listed by: OMICtools is related to: InterProScan |
PMID:16769687 | Free | OMICS_00562 | SCR_013457 | RARTF: RIKEN Arabidopsis Transcription Factor database, RIKEN Arabidopsis Transcription Factor database | 2026-02-14 02:06:25 | 2 | ||||||
|
miRWalk Resource Report Resource Website 1000+ mentions |
miRWalk (RRID:SCR_016509) | data or information resource, database | Software tool to store the predicted and the experimentally validated microRNA (miRNA)-target interaction pairs. Predictions within the complete sequence of genes of human, mouse, and rat genomes. Integrates a comparative platform of miRNA-binding sites resulting from ten different prediction datasets. | microRNA, target, interaction, pair, binding, site, sequence, gene, data, FASEB list | is listed by: OMICtools | PMID:26226356 | Free, Available for download, Freely available | SCR_016509 | 2026-02-14 02:06:47 | 1180 | |||||||||
|
CGEN Resource Report Resource Website 10+ mentions |
CGEN (RRID:SCR_001251) | CGEN | software application, data processing software, data analysis software, software resource | 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 | 2026-02-15 09:18:04 | 17 | ||||||
|
GenoSet Resource Report Resource Website |
GenoSet (RRID:SCR_001275) | GenoSet | software application, data processing software, data analysis software, software resource | Software package to load, manipulate, and plot copynumber and BAF data by providing classes similar to ExpressionSet for copy number analysis. The class extends ExpressionSet by adding a locData slot for a RangedData or GRanegs object. This object contains feature genome location data and provides for efficient subsetting on genome location. CNSet and BAFSet extend GenoSet and require assayData matrices for Copy Number (cn) or Log-R Ratio (lrr) and B-Allele Frequency (baf) data. Implements and provides convenience functions for processing of copy number and B-Allele Frequency data. | copy number variation, data representation, infrastructure, microarray, snp |
is listed by: OMICtools has parent organization: Bioconductor |
Artistic License, v2 | OMICS_02063 | SCR_001275 | genoset - Provides classes similar to ExpressionSet for copy number analysis | 2026-02-15 09:18:04 | 0 |
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