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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | ||||||||
|
InsertionMapper Resource Report Resource Website |
InsertionMapper (RRID:SCR_004163) | InsertionMapper | software resource | A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. It consists of four independently working modules: Data Preprocessing, Database Modeling, Dimension Deconvolution and Element Mapping. This pipeline tool is applicable to scenarios requiring analysis of the tremendous output of short reads produced in NGS sequencing experiments of targeted genome sequences. | high throughput sequencing, dna sequence, next generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Montclair State University; New Jersey; USA |
PMID:24090499 | Acknowledgement requested, GNU General Public License | OMICS_01547, biotools:insertionmapper | https://bio.tools/insertionmapper | SCR_004163 | 2026-08-01 12:02:38 | 0 | ||||||
|
CB-Commander Resource Report Resource Website |
CB-Commander (RRID:SCR_004237) | CB-Commander | software resource | A plugin based software tool that tries to integrate high throughput sequencing algorithms. It allows researchers to design and execute their experiments through a user friendly interface, enabling users to integrate di erent components of an experiment, e.g. algorithms and converters, into one graphically interfaced application that is very easy to use when working on remote servers as well as local computers. The graphical user interface facilitates a visual design of experiments by using a block diagram to represent the components (algorithms, converters, etc.) of an experiment as a pipeline. The users can easily modify this pipeline. | java, java swing, high throughput sequencing |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Simon Fraser University; British Columbia; Canada |
GNU General Public License, v2 | OMICS_01534 | http://sourceforge.net/projects/cb-commander/ | SCR_004237 | 2026-08-01 12:02:33 | 0 | |||||||
|
PASHA Resource Report Resource Website 10+ mentions |
PASHA (RRID:SCR_004455) | PASHA | software resource | A parallel short read assembler for large genomes using de Bruijn graphs. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21867511 | OMICS_00024 | SCR_004455 | 2026-08-01 12:02:36 | 10 | |||||||||
|
SnoopCGH Resource Report Resource Website 1+ mentions |
SnoopCGH (RRID:SCR_004420) | SnoopCGH | software resource | A java desktop application for visualising and exploring comparative genomic hybridization (CGH) data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:19687029 | biotools:snoopcgh, OMICS_00736 | https://bio.tools/snoopcgh | SCR_004420 | 2026-08-01 12:02:41 | 2 | |||||||
|
LMAT Resource Report Resource Website 10+ mentions |
LMAT (RRID:SCR_004646) | LMAT | software resource | Open-source software tool to assign taxonomic labels to as many reads as possible in very large metagenomic datasets and report the taxonomic profile of the input sample. The quick "single pass" analysis of every read allows read binning to support additional more computationally expensive analysis such as metagenomic assembly or sensitive database searches on targeted subsets of reads. | c++, metagenomic, metagenomic classification, genome, virus, taxonomy, database, reference genome |
is listed by: OMICtools has parent organization: Lawrence Livermore National Laboratory has parent organization: SourceForge |
PMID:23828782 | Open unspecified license | OMICS_02285 | SCR_004646 | Livermore Metagenomics Analysis Toolkit | 2026-08-01 12:02:43 | 15 | ||||||
|
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 | ||||||
|
SobekCM Resource Report Resource Website |
SobekCM (RRID:SCR_003225) | SobekCM | software resource | Digital repository software written in C# / ASP.net for powering digital libraries in a Windows server environment. Standards-based repository keeps all files in METS/MODS packages. Several related applications are available as well and the libraries can work independently as great digital library resources. SobekCM allows users to discover online resources via semantic and full-text searches, as well as a variety of different browse mechanisms. For each digital resource in the repository there are a plethora of display options, which may be selected by an appropriately authenticated use. This repository includes online metadata editing and online submissions in support of institutional repositories. | archiving, resource management, metadata standard, ontology, data repository, research object, c#, windows |
is listed by: FORCE11 has parent organization: University of Florida; Florida; USA has parent organization: Google Code has parent organization: SourceForge |
NEH ; NSF ; NHPRC ; IMLS |
Free, Available for download, Freely available | nlx_157266 | SCR_003225 | SobekCM Digital Repository Software, SobekCM : Digital Content Management System, SobekCM Digital Repository | 2026-08-01 12:02:28 | 0 | ||||||
|
mrsFAST Resource Report Resource Website 10+ mentions |
mrsFAST (RRID:SCR_003128) | mrsFAST | software resource | A cache-oblivious algorithm designed to map short reads to reference genome assemblies in a fast and memory-efficient manner. It optimizes cache usage to get higher performance. Currently Supported Features: * Mistmatches, No indels * Paired-end Mapping Mode * Discordant Paired-end Mapping Mode (to be used in conjuction with Variation Hunter) | next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SPLITREAD has parent organization: SourceForge |
PMID:20676076 | Free, Available for download, Freely available | biotools:mrsfast, nlx_156780 | https://bio.tools/mrsfast | SCR_003128 | mrsFAST: micro-read substitution-only Fast Alignment Search Tool, micro-read substitution-only Fast Alignment Search Tool | 2026-08-01 12:02:03 | 20 | |||||
|
SpliCQ Resource Report Resource Website |
SpliCQ (RRID:SCR_003266) | SpliCQ | software resource | A Java software package which allows for the identification of splicing events and differentially expressed isoforms in next generation sequencing data. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_01341 | SCR_003266 | 2026-08-01 12:02:07 | 0 | ||||||||
|
ORFprimer Resource Report Resource Website 1+ mentions |
ORFprimer (RRID:SCR_003269) | ORFprimer | software resource | An extended software package for high throughput PCR primer design for biological sequences. It reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number. | java, java swing, open reading frame, protein, high throughput sequencing, primer, primer design, pcr, pcr primer design |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02331 | SCR_003269 | ORFprimer - primer design for ORFs | 2026-08-01 12:02:07 | 1 | |||||||
|
Gemi Resource Report Resource Website 10+ mentions |
Gemi (RRID:SCR_003211) | Gemi | software resource | Automated software tool to design polymerase chain reaction (PCR) primers. It accepts multiple aligned and long sequences with degenerated nucleotides. It can be used for quantitative/real-time PCR, conventional and Sanger sequencing. Gemi accepts DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). The programs are as the following: # The first program is to design PCR primers from multiple sequence alignment. # Program to convert ClustalW format (.aln), Phylip (.phy) and (.gde) formats to Fasta format. # Reverse and/or complement program is to find the reverse and complement counterpart of single or multiple sequences. | polymerase chain reaction, primer, pcr primer design, pcr primer, dna sequence, rna sequence, c#, .net/mono, windows, probe, multiple aligned sequence |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23316117 | Free, Available for download, Freely available | OMICS_02332 | SCR_003211 | Gemi - PCR oligos / primers design from multiple sequence alignments | 2026-08-01 12:02:18 | 13 | ||||||
|
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 | ||||||
|
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 |
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.
