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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
CoRAL - Classification of RNAs by Analysis of Length Resource Report Resource Website 1+ mentions |
CoRAL - Classification of RNAs by Analysis of Length (RRID:SCR_010828) | CoRAL | software resource | A machine learning software package that can predict the precursor class of small RNAs present in a high-throughput RNA-sequencing dataset. In addition to classification, it also produces information about the features that are most important for discriminating different populations of small non-coding RNAs. |
is listed by: OMICtools has parent organization: University of Pennsylvania; Philadelphia; USA |
PMID:23700308 | Acknowledgement requested | OMICS_00372 | SCR_010828 | Classification of RNAs by Analysis of Length | 2026-08-01 12:04:16 | 8 | |||||||
|
PriVar Resource Report Resource Website 1+ mentions |
PriVar (RRID:SCR_010784) | PriVar | software resource | A toolkit for prioritizing SNVs and indels from next-generation sequencing data. | is listed by: OMICtools | OMICS_00160 | SCR_010784 | 2026-08-01 12:04:16 | 2 | ||||||||||
|
CNVer Resource Report Resource Website 1+ mentions |
CNVer (RRID:SCR_010820) | CNVer | software resource | A method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:cnver, OMICS_00341 | https://bio.tools/cnver | SCR_010820 | 2026-08-01 12:04:17 | 8 | ||||||||
|
CNVnator Resource Report Resource Website 500+ mentions |
CNVnator (RRID:SCR_010821) | CNVnator | software resource | An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. | is listed by: OMICtools | OMICS_00343 | SCR_010821 | 2026-08-01 12:03:58 | 510 | ||||||||||
|
Diplotyper Resource Report Resource Website |
Diplotyper (RRID:SCR_010789) | Diplotyper | software resource | A fully automated software tool which is available for Linux to investigate associations between a diplotype group and a phenotype in linear or logistic regression. |
is listed by: OMICtools has parent organization: Google Code |
OMICS_00195 | SCR_010789 | 2026-08-01 12:04:17 | 0 | ||||||||||
|
Control-FREEC Resource Report Resource Website 100+ mentions |
Control-FREEC (RRID:SCR_010822) | Control-FREEC | software resource | Prediction of copy number alterations and loss of heterozygosity using deep-sequencing data. | is listed by: OMICtools | OMICS_00344 | SCR_010822 | 2026-08-01 12:04:16 | 327 | ||||||||||
|
readDepth Resource Report Resource Website 10+ mentions |
readDepth (RRID:SCR_010824) | readDepth | software resource | This package for R can detect copy number aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome. | is listed by: OMICtools | OMICS_00350 | SCR_010824 | 2026-08-01 12:03:58 | 23 | ||||||||||
|
HapCUT Resource Report Resource Website 10+ mentions |
HapCUT (RRID:SCR_010791) | HapCUT | software resource | A max-cut based algorithm for haplotype assembly using sequence reads from the two chromosomes of an individual. | is listed by: OMICtools | OMICS_00198 | SCR_010791 | 2026-08-01 12:04:16 | 17 | ||||||||||
|
Relate Resource Report Resource Website 10+ mentions |
Relate (RRID:SCR_010794) | Relate | software resource | Software providing a method that estimates the probability of sharing alleles identity by descent (IBD) across the genome and can also be used for mapping disease loci using distantly related individuals. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:19025785 | biotools:relateadmix, OMICS_00207 | https://bio.tools/relateadmix | SCR_010794 | 2026-08-01 12:04:16 | 44 | |||||||
|
National Institute of Genetics; Shizuoka; Japan Resource Report Resource Website |
National Institute of Genetics; Shizuoka; Japan (RRID:SCR_010836) | institution | Institute for genetics, through National BioResource Project, collects, preserves, and provides bio-resources (strains, populations, tissues, cells, genes of animals, plants and microorganisms, and information on these materials for R&D use) that are essential for life science research. | RIN, Resource Information Network, strains, populations, tissues, cells, genes of animals, plants and microorganisms, RRID Community Authority |
is listed by: Resource Information Network is parent organization of: Genome Network Platform is parent organization of: DNA DataBank of Japan (DDBJ) is parent organization of: NEXTDB is parent organization of: RAP-DB is parent organization of: Alternate Splicing - induced ALteration of Protein Structure is parent organization of: GTOP - Genomes To Protein structures is parent organization of: Protein Mutant Database works with: International Mouse Strain Resource |
nlx_92390 | SCR_010836 | NIG | 2026-08-01 12:04:16 | 0 | |||||||||
|
RNAsnp Resource Report Resource Website 10+ mentions |
RNAsnp (RRID:SCR_010837) | RNAsnp | data analysis service, service resource, production service resource, software resource, analysis service resource | Software / Web Server to predict the effect of SNPs on local RNA secondary structure based on the RNA folding algorithms implemented in the Vienna RNA package. |
is listed by: OMICtools has parent organization: University of Copenhagen; Copenhagen; Denmark |
PMID:23630321 | OMICS_00392 | SCR_010837 | RNAsnp Web Server, RNAsnp Web Server: Predicting SNP effects on local RNA secondary structure | 2026-08-01 12:04:17 | 32 | ||||||||
|
BCmicrO Resource Report Resource Website 1+ mentions |
BCmicrO (RRID:SCR_010838) | BCmicrO | software resource, web application | A Bayesian decision fusion algorithm for microRNA target prediction that combines the prediction of TargetScan, miRanda, PicTar, mirTarget, PITA, and DianamicroT. Users enter a Ref_seq ID for a query target gene and select a miRNA, which BCmicrO will use in its predictive algorithm. The prediction results can then be downloaded. | mirna, microrna, bayesian, decision fusion algorithm, computational target prediction algorithm, web application, |
is listed by: OMICtools has parent organization: University of Texas at San Antonio; Texas; USA |
Public | OMICS_00393 | SCR_010838 | 2026-08-01 12:03:58 | 7 | ||||||||
|
miRExpress Resource Report Resource Website 10+ mentions |
miRExpress (RRID:SCR_010831) | miRExpress | software resource | A stand-alone software package implemented for generating miRNA expression profiles from high-throughput sequencing of RNA without the need for sequenced genomes. |
is listed by: OMICtools has parent organization: National Chiao Tung University; Hsinchu; Taiwan |
OMICS_00379 | SCR_010831 | 2026-08-01 12:03:58 | 49 | ||||||||||
|
HugeSeq Resource Report Resource Website 10+ mentions |
HugeSeq (RRID:SCR_010803) | HugeSeq | software resource | An automated pipeline for detecting genetic variants from High-throUghput GEnome SEQuencing. | is listed by: OMICtools | OMICS_00288 | SCR_010803 | 2026-08-01 12:04:16 | 10 | ||||||||||
|
MutFinder Resource Report Resource Website |
MutFinder (RRID:SCR_010804) | MutFinder | software resource | It streamlines the next generation sequencing data analysis using BFAST for aligner, SAMTOOLS for SNP caller, and ANNOVAR for annotation. |
is listed by: OMICtools has parent organization: Google Code |
OMICS_00290 | SCR_010804 | Mutation finder in DNA-seq | 2026-08-01 12:04:17 | 0 | |||||||||
|
SIMPLEX Resource Report Resource Website 10+ mentions |
SIMPLEX (RRID:SCR_010807) | SIMPLEX | software resource | Cloud-enabled pipeline for the comprehensive analysis of exome sequencing data. | is listed by: OMICtools | OMICS_00294 | SCR_010807 | 2026-08-01 12:04:16 | 21 | ||||||||||
|
WEP Resource Report Resource Website |
WEP (RRID:SCR_010809) | WEP | software resource | A complete whole-exome sequencing pipeline and provides easy access through interface to intermediate and final results. | is listed by: OMICtools | OMICS_00296 | SCR_010809 | 2026-08-01 12:03:57 | 0 | ||||||||||
|
MoDIL Resource Report Resource Website 1+ mentions |
MoDIL (RRID:SCR_010764) | MoDIL | software resource | Software for a novel method for finding medium sized indels from high throughput sequencing datasets. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Toronto; Ontario; Canada |
OMICS_00066, biotools:modil | https://bio.tools/modil | SCR_010764 | MoDIL: Detecting INDEL Variation with Clone-end Sequencing | 2026-08-01 12:04:15 | 4 | |||||||
|
MISA Resource Report Resource Website 500+ mentions |
MISA (RRID:SCR_010765) | MISA | software resource | Software tool that allows the identification and localization of perfect microsatellites as well as compound microsatellites which are interrupted by a certain number of bases. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00110, biotools:misa | https://bio.tools/misa | SCR_010765 | MISA - MIcroSAtellite identification tool | 2026-08-01 12:04:17 | 941 | |||||||
|
T-REKS Resource Report Resource Website 10+ mentions |
T-REKS (RRID:SCR_010768) | T-REKS | software resource | An algorithm for de novo detection and alignment of repeats in sequences based on K-means algorithm. | matlab | is listed by: OMICtools | PMID:19671691 | OMICS_00116 | SCR_010768 | 2026-08-01 12:04:17 | 17 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
