Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
GEOSS Resource Report Resource Website 1+ mentions |
GEOSS (RRID:SCR_003401) | GEOSS | software resource | A complete software system used to store and analyze gene expression data. |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of Virginia; Virginia; USA |
Free, Freely available | OMICS_00764 | SCR_003401 | Gene Expression Open Source System, GEOSS - Gene Expression Open Source System, GEOSS Gene Expression Open Source System, GeneX Va | 2026-08-01 12:02:20 | 1 | ||||||||
|
Amplicon Resource Report Resource Website 1000+ mentions |
Amplicon (RRID:SCR_003294) | Amplicon | software resource | Software tool for designing PCR primers on aligned groups of DNA sequences. The most important application is the design of "group-specific" PCR primer sets that amplify a DNA region from a given taxonomic group but do not amplify orthologous regions from other taxonomic groups. It is written in Python 2.3 and Tkinter 8.4. The current script was created for Windows and an executable is available. Future versions of the script should be able to run on Linux and Mac | python, pcr primer, pcr, primer, tkinter, windows, dna sequence |
is listed by: OMICtools has parent organization: SourceForge |
PMID:14962918 | Free, Available for download, Freely available | OMICS_02329 | http://www.aad.gov.au/amplicon | SCR_003294 | 2026-08-01 12:02:19 | 1673 | ||||||
|
GEPAT Resource Report Resource Website 1+ mentions |
GEPAT (RRID:SCR_003597) | GEPAT | software resource | A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:17543125 | OMICS_00765, biotools:gepat | https://bio.tools/gepat | SCR_003597 | Genome Expression Pathway Analysis Tool | 2026-08-01 12:02:15 | 2 | ||||||
|
DMET-Analyzer Resource Report Resource Website 1+ mentions |
DMET-Analyzer (RRID:SCR_002030) | DMET-Analyzer | software resource | Software tool for the automatic association analysis among the variation of the patient genomes and the clinical conditions of patients, i.e. the different response to drugs. The system allows: (i) to automatize the workflow of analysis of DMET (drug metabolism enzymes and transporters)-SNP (Single Nucleotide Polymorphism) data avoiding the use of multiple tools; (ii) the automatic annotation of DMET-SNP data and the search in existing databases of SNPs (e.g. dbSNP), (iii) the association of SNP with pathway through the search in PharmaKGB, a major knowledge base for pharmacogenomic studies. It has a simple graphical user interface that allows users (doctors/biologists) to upload and analyze DMET files produced by Affymetrix DMET-Console in an interactive way. | drug, metabolism, enzyme, transporter, affymetrix, variation, genome, clinical, affymetrix dmet, single nucleotide polymorphism, annotation, analysis, pharmacogenomic, pathway |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23035929 | Free, Available for download, Freely available | OMICS_01920 | SCR_002030 | DMETANALYZER, DMETANALYZER - A tool for supporting pharmacogenomics data analysis | 2026-08-01 12:02:07 | 1 | ||||||
|
Ray Resource Report Resource Website 1+ mentions |
Ray (RRID:SCR_001916) | Ray | software resource | Software that assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2. | mpi, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:20958248 DOI:10.1089/cmb.2009.0238 |
Free, Available for download, Freely available | OMICS_00027, biotools:ray | https://bio.tools/ray, https://sources.debian.org/src/ray/ | SCR_001916 | Ray - a de novo assembler using MPI 2.2, Ray - Parallel genome assemblies for parallel DNA sequencing | 2026-08-01 12:01:55 | 1 | |||||
|
Cake Resource Report Resource Website 10+ mentions |
Cake (RRID:SCR_002133) | software resource | A bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone. | standalone software, unix/linux, mac os x, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23803469 | Free, Available for download, Freely available | OMICS_03613, biotools:cake | https://bio.tools/cake | SCR_002133 | 2026-08-01 12:01:42 | 11 | |||||||
|
Matchprot Resource Report Resource Website |
Matchprot (RRID:SCR_002163) | software resource | A pairwise protein structure alignment software. | standalone software, c |
is listed by: OMICtools has parent organization: SourceForge |
PMID:17338826 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_03666 | SCR_002163 | 2026-08-01 12:02:00 | 0 | ||||||||
|
USeq Resource Report Resource Website 100+ mentions |
USeq (RRID:SCR_004753) | USeq | software resource | A collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_00499, biotools:useq | https://bio.tools/useq | SCR_004753 | 2026-08-01 12:02:45 | 124 | ||||||||
|
SVMerge Resource Report Resource Website 10+ mentions |
SVMerge (RRID:SCR_004777) | SVMerge | software resource | Software pipeline to detect structural variants (SVs) by integrating calls from several existing SV callers, which are then validated and the breakpoints refined using local de novo assembly. The output is in BED format allowing for easy downstream analysis or viewing in a genome browser. It is modular and extensible allowing new callers to be incorporated as they become available. | structural variant, breakpoint, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:21194472 | biotools:svmerge, OMICS_00325 | https://bio.tools/svmerge | SCR_004777 | SVMerge - Enhanced structural variant and breakpoint detection | 2026-08-01 12:02:40 | 19 | ||||||
|
T-lex Resource Report Resource Website 1+ mentions |
T-lex (RRID:SCR_005134) | T-lex | software resource | Software package for fast and accurate discovery, annotation, re-annotation and population analysis of Transposable Elements using Next-Generation Sequencing data. | transposable element, next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California has parent organization: SourceForge |
GNU General Public License | biotools:t-lex2, OMICS_00121 | https://bio.tools/t-lex2 | SCR_005134 | T-lex package | 2026-08-01 12:02:46 | 4 | ||||||
|
GESND Resource Report Resource Website |
GESND (RRID:SCR_005179) | GESND | software resource | A software package and a pipeline for identifying causal mutations for rare congenital diseases by next-generation sequencing. Features * one-stop solution for identifying causal mutations of rare genetic diseases * detect wide-spctrum variants, including medium and large sized indels, and tandem repeats * annotate and filter variants * prioritize candidate variants | next-generation sequencing, mutation, variant, indel, tandem repeat |
is listed by: OMICtools has parent organization: SourceForge |
Rare congenital disease | OMICS_00175 | SCR_005179 | Genetic Screening and Diagnosis, GESND - Genetic Screening and Diagnosis | 2026-08-01 12:02:47 | 0 | |||||||
|
AnnTools Resource Report Resource Website 1+ mentions |
AnnTools (RRID:SCR_005170) | AnnTools | software resource | Software tool for annotating single nucleotide substitutions (SNP/SNV), small insertions/deletions (indels), and copy number variations (CNV) calls generated from sequencing and microarray data. Only human genome build 37/hg19 can be annotated at this time. | single nucleotide substitution, snp, snv, indel, copy number variation, sequencing, microarray, linux, unix, mac osx, python, mysql, genome annotation, genome, annotation |
is listed by: OMICtools has parent organization: SourceForge |
BSD License | OMICS_00166 | SCR_005170 | 2026-08-01 12:02:50 | 4 | ||||||||
|
HIVCD Resource Report Resource Website |
HIVCD (RRID:SCR_005201) | HIVCD | software resource | Informatics software tool to identify patient sequences that are too similar to happen by chance alone. Highly similar sequences are likely to occur from contamination or other situations like geographic linkage. | java, perl, contamination, sequencing, error, pairwise comparison, testing, analysis, contamination screening |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23583427 | Apache License, v2 | OMICS_00220 | SCR_005201 | HIVCD - Informatics tool for contamination screening in the HIV sequencing lab, HIV Contamination Detection | 2026-08-01 12:02:50 | 0 | ||||||
|
ASOoViR Resource Report Resource Website |
ASOoViR (RRID:SCR_005161) | ASOoViR | software resource | A set of Ruby modules to annotate consequence terms, defined by the Sequence Ontology, of variants (SNP/SNVs, INDELs, SVs, CNAs) using Ensembl gene sets. Prior to annotation of variants an Ensembl gene set and reference coding sequences are loaded into memory from a database file, which can be downloaded or generated by the user from reference files. This allows rapid annotation of variants, making it suitable for annotation of whole genome scale calls. Annotation is performed on a transcript level basis, identifying associated sequence ontology terms for affected and nearby transcripts. Default output can be obtained on a gene basis, summarising the consequences for each gene affected, or on a transcript level basis. Output information is also readily customisable using user-generated scripts. | ruby, annotate |
is listed by: OMICtools is related to: SO has parent organization: SourceForge |
OMICS_00167 | SCR_005161 | Annotating Sequence Ontology of Variants in Ruby, ASOoViR - Annotating Sequence Ontology of Variants in Ruby | 2026-08-01 12:02:56 | 0 | ||||||||
|
SnpEff Resource Report Resource Website 5000+ mentions |
SnpEff (RRID:SCR_005191) | SnpEff | software resource | Genetic variant annotation and effect prediction software toolbox that annotates and predicts effects of variants on genes (such as amino acid changes). By using standards, such as VCF, SnpEff makes it easy to integrate with other programs. | genome, genetic variant, annotation, effect, variant, gene, cancer variant, gatk, hgsv, single nucleotide polymorphisms, genome sequence, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: GATK has parent organization: SourceForge has parent organization: Wayne State University; Michigan; USA works with: SnpSift |
Cancer | PMID:22728672 | Free, Freely available | biotools:snpeff, OMICS_00186 | https://bio.tools/snpeff, https://sources.debian.org/src/snpeff/ | SCR_005191 | SnpEff - Genetic variant annotation and effect prediction toolbox | 2026-08-01 12:02:57 | 5186 | ||||
|
inGAP Resource Report Resource Website 10+ mentions |
inGAP (RRID:SCR_005261) | inGAP | software resource | Software mining pipeline guided by a Bayesian principle to detect single nucleotide polymorphisms, insertion and deletions by comparing high-throughput pyrosequencing reads with a reference genome of related organisms. This pipeline is extended to identify and visualize large-size structural variations, including insertions, deletions, inversions and translocations. | structural variation, genome, next-generation sequence, genome analysis, alignment, single nucleotide polymorphism, insertion, deletion, indel, inversion, translocation, windows, linux, macos/x, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Fudan University; Shanghai; China has parent organization: Chinese Academy of Sciences; Beijing; China |
OMICS_00319, biotools:ingap | https://bio.tools/ingap | SCR_005261 | inGAP-sv, inGAP-sv: structural variation detection and visualization, integrative next-generation genome analysis pipeline | 2026-08-01 12:02:49 | 29 | |||||||
|
CoverageCalculator Resource Report Resource Website 1+ mentions |
CoverageCalculator (RRID:SCR_005352) | CoverageCalculator | software resource | Small and very fast utility to calculate X-coverage from Next-Generation-Sequencing data. | next-generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01164 | SCR_005352 | 2026-08-01 12:02:52 | 2 | |||||||||
|
mrFAST Resource Report Resource Website 10+ mentions |
mrFAST (RRID:SCR_005487) | mrFAST | software resource | Software designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient mannerl. Currently Supported Features: * Output in SAM format * Indels up to 8 bp (4 bp deletions and 4 bp insertions) * Paired-end mapping ** Discordant option to generate mapping file ready for VariationHunter to detect structural variants. * One end anchored (OEA) map locations for novel sequence insertion detection with NovelSeq * Matepair library mapping (long inserts with RF orientation). Planned Features: * Multithreading | next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: SPLITREAD has parent organization: SourceForge |
PMID:19718026 | biotools:mrfast, OMICS_00671 | https://bio.tools/mrfast | SCR_005487 | mrFAST - Micro Read Fast Alignment Search Tool, Micro Read Fast Alignment Search Tool | 2026-08-01 12:02:54 | 16 | ||||||
|
CUSHAW2-GPU Resource Report Resource Website |
CUSHAW2-GPU (RRID:SCR_005480) | CUSHAW2-GPU | software resource | Software program (based on CUSHAW2) designed and optimized for Kepler-based GPUs, but still workable on earlier-generation Fermi-based ones. | c++, genome, alignment |
is listed by: OMICtools is related to: CUSHAW has parent organization: SourceForge |
Apache License | OMICS_00659 | SCR_005480 | 2026-08-01 12:02:59 | 0 | ||||||||
|
CUSHAW Resource Report Resource Website 1+ mentions |
CUSHAW (RRID:SCR_005479) | CUSHAW | software resource | Software package for next-generation sequencing read alignment that is fast and parallel gapped read alignment to large genomes, such as the human genome. | next-generation sequencing, read alignment, genome, alignment |
is listed by: OMICtools is related to: CUSHAW2-GPU has parent organization: Johannes Gutenberg University Mainz; Rhineland-Palatinate; Germany has parent organization: SourceForge |
PMID:22576173 PMID:24466273 |
OMICS_00658 | SCR_005479 | CUSHAW2, CUSHAW3 | 2026-08-01 12:02:54 | 2 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
