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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
vipR Resource Report Resource Website 50+ mentions |
vipR (RRID:SCR_010685) | vipR | software resource | A software program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00081 | SCR_010685 | 2025-02-14 10:31:36 | 56 | ||||||||||
|
MaSuRCA Resource Report Resource Website 100+ mentions |
MaSuRCA (RRID:SCR_010691) | MaSuRCA | software resource | A whole genome assembly software that combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Maryland; Maryland; USA |
OMICS_00020, biotools:masurca | https://bio.tools/masurca | SCR_010691 | 2025-02-14 10:31:36 | 413 | ||||||||
|
Gossamer Resource Report Resource Website |
Gossamer (RRID:SCR_010612) | Gossamer | software resource | A software application for the de novo assembly of genomes from fragments of DNA that specifically attacks the question of scalability. | is listed by: OMICtools | OMICS_00017 | SCR_010612 | Gossamer: A Space-Efficient Genome Assembler | 2025-02-14 10:31:36 | 0 | |||||||||
|
Meraculous Resource Report Resource Website 10+ mentions |
Meraculous (RRID:SCR_010700) | Meraculous | software resource | An algorithm for de novo genome assembly with short paired-end reads. | is listed by: OMICtools | OMICS_00021 | SCR_010700 | Meraculous: De Novo Genome Assembly with Short Paired-End Reads | 2025-02-14 10:31:36 | 38 | |||||||||
|
ContextMap Resource Report Resource Website 10+ mentions |
ContextMap (RRID:SCR_010496) | ContextMap | software resource | A context-based approach to identify the most likely mapping for RNA-seq experiments. | is listed by: OMICtools | OMICS_01239 | SCR_010496 | 2025-02-14 10:31:35 | 24 | ||||||||||
|
CRAC Resource Report Resource Website 10+ mentions |
CRAC (RRID:SCR_010652) | CRAC | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Integrated RNA-Seq read analysis. |
is listed by: OMICtools is listed by: Debian |
DOI:10.1186/s12920-016-0178-5 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01240 | https://sources.debian.org/src/crac/ | SCR_010652 | 2025-02-14 10:31:36 | 16 | |||||||
|
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 | 2025-02-14 10:31:59 | 6 | |||||||
|
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 | 2025-02-14 10:31:38 | 1 | ||||||||||
|
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 | 2025-02-14 10:31:46 | 8 | ||||||||
|
CNVnator Resource Report Resource Website 100+ 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 | 2025-02-14 10:31:39 | 448 | ||||||||||
|
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 | 2025-02-14 10:31:38 | 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 | 2025-02-14 10:31:59 | 286 | ||||||||||
|
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 | 2025-02-14 10:31:46 | 19 | ||||||||||
|
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 | 2025-02-14 10:31:38 | 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 | 2025-02-14 10:31:45 | 34 | |||||||
|
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 | 2025-02-14 10:31:39 | 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 | 2025-02-14 10:31:38 | 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 | 2025-02-14 10:31:45 | 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 | 2025-02-14 10:31:45 | 18 | ||||||||||
|
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 | 2025-02-14 10:31:59 | 0 |
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