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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
CanPredict Resource Report Resource Website 1+ mentions |
CanPredict (RRID:SCR_008216) | CanPredict | analysis service resource, data analysis service, production service resource, service resource | Web application that uses a combination of computational methods to identify those changes most likely to be cancer-associated. |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA |
Cancer | OMICS_00142 | SCR_008216 | CanPredict: A computational tool for predicting Cancer-associated mutations | 2026-08-08 12:04:20 | 3 | ||||||||
|
Gene Array Analyzer Resource Report Resource Website 1+ mentions |
Gene Array Analyzer (RRID:SCR_008323) | GAA | analysis service resource, data analysis service, production service resource, service resource | Data analysis service that allows to process CEL files from Affymetrix, Inc. GeneChip Gene 1.0 ST Arrays to identify alternative splicing. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22123740 | Acknowledgement requested | OMICS_00759, biotools:gene_array_analyzer | https://bio.tools/gene_array_analyzer | SCR_008323 | 2026-08-08 12:04:14 | 5 | ||||||
|
DARIO Resource Report Resource Website 10+ mentions |
DARIO (RRID:SCR_008600) | DARIO | analysis service resource, data analysis service, production service resource, service resource | A free web server for the analysis of short RNAs from high throughput sequencing data. | is listed by: OMICtools | PMID:21622957 | OMICS_00356 | SCR_008600 | 2026-08-08 12:04:22 | 10 | |||||||||
|
ExpressYourself Resource Report Resource Website |
ExpressYourself (RRID:SCR_008881) | ExpressYourself | analysis service resource, data analysis service, production service resource, service resource | A fully integrated platform for processing microarray data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00755, biotools:expressyourself | https://bio.tools/expressyourself | SCR_008881 | ExpressYourself: microarray data processing platform, Express Yourself, Express Yourself: microarray data processing platform | 2026-08-08 12:04:23 | 0 | |||||||
|
RNA-Seq Blog Resource Report Resource Website 1+ mentions |
RNA-Seq Blog (RRID:SCR_010025) | RNA-Seq Blog | data or information resource, blog, narrative resource | Blog presenting news and information, and spur discussion about topics related to RNA-Seq. | is listed by: OMICtools | OMICS_01722 | SCR_010025 | 2026-08-08 12:04:24 | 1 | ||||||||||
|
isomiRex Resource Report Resource Website 1+ mentions |
isomiRex (RRID:SCR_009521) | isomiRex | analysis service resource, data analysis service, production service resource, service resource | A web tool for the identification of microRNAs and their isomiRs, as well as differential expression from NGS datasets. | is listed by: OMICtools | PMID:23831580 | OMICS_00359 | SCR_009521 | 2026-08-08 12:04:17 | 4 | |||||||||
|
MicroSNiPer Resource Report Resource Website 10+ mentions |
MicroSNiPer (RRID:SCR_009880) | MicroSNiPer | analysis service resource, data analysis service, production service resource, service resource | A web-based application which predicts the impact of a SNP on putative microRNA targets. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: National Institute of Mental Health |
PMID:20809528 | biotools:microsniper, OMICS_00388 | https://bio.tools/microsniper | SCR_009880 | 2026-08-08 12:04:24 | 18 | |||||||
|
mirTools Resource Report Resource Website 10+ mentions |
mirTools (RRID:SCR_009701) | mirTools | analysis service resource, data analysis service, production service resource, service resource | A comprehensive web server developed to allow researchers to comprehensively characterize small RNA transcriptome. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23778453 | OMICS_00365, biotools:mirtools | https://bio.tools/mirtools | SCR_009701 | mirTools 2.0 | 2026-08-08 12:04:25 | 13 | ||||||
|
DIANA-LncBase Resource Report Resource Website 100+ mentions |
DIANA-LncBase (RRID:SCR_010840) | LncBase | database, data or information resource | Database that hosts elaborated information for both predicted and experimentally verified, miRNA-lncRNA interactions. The database consists of two distinct modules. The Experimental Module contains detailed information for more than 5,000 interactions, between 2,958 lncRNAs and 120 miRNAs, ranging from miRNA and lncRNA related facts to information specific to their interaction, the experimental validation methodologies and their outcomes. The Prediction Module, which is based on the latest version of DIANA-microT target prediction algorithm (DIANA-microT-CDS), contains detailed information for more than 10 million interactions, between 56,097 lncRNAs and 3,078 miRNAs, ranging from miRNA and lncRNA related details to specific information regarding their interaction sites, graphical representation of their binding and the predicted score. This module exhibits a unique feature for searching the database. Users are able to add genomic locations to their queries thus browsing every miRNA-lncRNA interaction that has at least one MRE located inside the queried locus. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23193281 | biotools:diana-lncbase, OMICS_00396 | https://bio.tools/diana-lncbase | SCR_010840 | 2026-08-08 12:04:28 | 169 | |||||||
|
HOCTAR Resource Report Resource Website 10+ mentions |
HOCTAR (RRID:SCR_010842) | HOCTAR | database, data or information resource | Database serving as a tool for microRNA target prediction. The HOCTAR procedure is based on the integration of expression profiling and sequence-based miRNA target recognition softwares. HOCTAR database (db) is the first and unique database to use transcriptomic data to score putative miRNA targets looking at the expression behaviour of their host genes, and it includes and re-analyzes all miRNA target predictions generated by softwares such as miRanda, TargetScan and PicTar. The HOCTARdb contains the prediction target lists for 290 human intragenic miRNAs and also provides tentative assignments of miRNA function based on Gene Ontology analyses of their predicted targets. There are two ways to interrogate HOCTARdb: (i) by selecting a miRNA using either an alphabetically sorted pull-down menu in the microRNA query, or (ii) by typing a target gene symbol (HUGO Gene Name-approved) in the Target Gene Name query. | microrna, target prediction. | is listed by: OMICtools | PMID:21435384 PMID:19088304 |
Public | OMICS_00398 | SCR_010842 | Host gene Opposite Correlated TARgets, HOCTARdb, HOCTAR database | 2026-08-08 12:04:27 | 11 | ||||||
|
MicroCosm Targets Resource Report Resource Website 500+ mentions |
MicroCosm Targets (RRID:SCR_010846) | MicroCosm Targets | database, data or information resource | Database of computationally predicted targets for microRNAs across many species. |
is listed by: OMICtools has parent organization: European Bioinformatics Institute |
OMICS_00400 | https://www.ebi.ac.uk/ | SCR_010846 | miRBase Targets | 2026-08-08 12:04:27 | 655 | ||||||||
|
AceDB Resource Report Resource Website 10+ mentions |
AceDB (RRID:SCR_010671) | database, data or information resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 6th,2023. Software genome database management system. | genome database management system, genome database, management system, |
is listed by: Debian is listed by: OMICtools is related to: ESTHER has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
DOI:10.1109/5992.764215 | THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_75315, OMICS_15828 | https://sources.debian.org/src/acedb-other/ | SCR_010671 | A C. elegans DataBase | 2026-08-08 12:04:26 | 12 | ||||||
|
miREval Resource Report Resource Website 10+ mentions |
miREval (RRID:SCR_010830) | miREval | analysis service resource, data analysis service, production service resource, service resource | A web tool for simple microRNA prediction in genome sequences. | is listed by: OMICtools | PMID:24048357 | OMICS_00378 | SCR_010830 | 2026-08-08 12:04:21 | 20 | |||||||||
|
PhenCode Resource Report Resource Website 1+ mentions |
PhenCode (RRID:SCR_010799) | PhenCode | database, data or information resource | A collaborative project to better understand the relationship between genotype and phenotype in humans that connects human phenotype and clinical data in various locus-specific mutation databases (LSDBs) with data on genome sequences, evolutionary history, and function in the UCSC Genome Browser. PhenCode is a collaboration among researchers at Penn State, UC Santa Cruz, and locus experts at other institutions. | genotype, phenotype, mutation |
is listed by: OMICtools is related to: UCSC Genome Browser has parent organization: Pennsylvania State University |
PMID:17326095 | Acknowledgement requested, Free | OMICS_00279 | SCR_010799 | PhenCode: Paving the Path between Phenotype and Genome, Phenotypes for ENCODE | 2026-08-08 12:04:28 | 7 | ||||||
|
Pscan-ChIP Resource Report Resource Website 1+ mentions |
Pscan-ChIP (RRID:SCR_010885) | Pscan-ChIP | analysis service resource, data analysis service, production service resource, service resource | Web server that, starting from a collection of genomic regions derived from a ChIP-Seq experiment, scans them using motif descriptors like JASPAR or TRANSFAC position-specific frequency matrices, or descriptors uploaded by users, and it evaluates both motif enrichment and positional bias within the regions according to different measures and criteria. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23748563 DOI:10.1093/nar/gkt448 |
biotools:pscanchip, OMICS_00490 | https://bio.tools/pscanchip, https://sources.debian.org/src/pscan-chip/ | SCR_010885 | 2026-08-08 12:04:21 | 6 | |||||||
|
SNP and indel Imputability Resource Report Resource Website 1+ mentions |
SNP and indel Imputability (RRID:SCR_010800) | SNP and indel Imputability | database, data or information resource | A comprehensive SNP and indel imputability database. |
is listed by: OMICtools has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
OMICS_00280 | SCR_010800 | 2026-08-08 12:04:27 | 1 | ||||||||||
|
CUPSAT Resource Report Resource Website 50+ mentions |
CUPSAT (RRID:SCR_010773) | CUPSAT | analysis service resource, data analysis service, production service resource, service resource | A tool to predict changes in protein stability upon point mutations. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:16845001 | biotools:cupsat, OMICS_00128 | https://bio.tools/cupsat | SCR_010773 | Cologne University Protein Stability Analysis Tool, CUPSAT: Cologne University Protein Stability Analysis Tool | 2026-08-08 12:04:21 | 86 | ||||||
|
LS-SNP/PDB Resource Report Resource Website 1+ mentions |
LS-SNP/PDB (RRID:SCR_010774) | LS-SNP/PDB | analysis service resource, data analysis service, production service resource, service resource | A web tool for genome-wide annotation of human SNPs. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Johns Hopkins University; Maryland; USA |
OMICS_00131, biotools:ls-snp | https://bio.tools/ls-snp | SCR_010774 | 2026-08-08 12:04:27 | 3 | ||||||||
|
LegumeTFDB Resource Report Resource Website 1+ mentions |
LegumeTFDB (RRID:SCR_010896) | LegumeTFDB | database, data or information resource | A public database that provides predicted transcription factor (TF) encoding genes annotated in genome sequences of three major legume species: soybean (Glycine max), Lotus japonicus and Medicago truncatula. | is listed by: OMICtools | PMID:19933159 | Free | OMICS_00556 | SCR_010896 | 2026-08-08 12:04:27 | 6 | ||||||||
|
mCSM Resource Report Resource Website 50+ mentions |
mCSM (RRID:SCR_010776) | mCSM | analysis service resource, data analysis service, production service resource, service resource | Data analysis service to the study of missense mutations which relies on graph-based signatures. | mutation, protein, protein stability, protein-protein, protein-dna, data set |
is listed by: OMICtools has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:24281696 | OMICS_00133 | SCR_010776 | mCSM: predicting the effect of mutations in proteins using graph-based signatures | 2026-08-08 12:04:28 | 81 |
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