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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Exonerate Resource Report Resource Website 100+ mentions |
Exonerate (RRID:SCR_016088) | alignment software, data processing software, image analysis software, software application, software resource, software toolkit | Software package for sequence alignment of pairwise sequence comparison. Exonerate can be used to align sequences using many alignment models, exhaustive dynamic programming, or a variety of heuristics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence, alignment, pairwise, comparison, dynamic, programming, heuristic, bio.tools |
is used by: ExonerateTransferAnnotation is listed by: Debian is listed by: bio.tools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:15713233 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:exonerate | https://bio.tools/exonerate | SCR_016088 | 2026-09-12 12:58:35 | 376 | |||||||
|
Bio++ Resource Report Resource Website 50+ mentions |
Bio++ (RRID:SCR_016055) | software application, software development tool, software library, software resource, software toolkit | Software providing a set of ready-to-use C++ libraries as re-usable tools to visualize, edit, print and output data for bioinformatics. It uses sequence analysis, phylogenetics, molecular evolution and population genetics to help to write programs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | phylogenetic, molecular evolution, genetic, program, write, tool, visualize, edit, print, data, bioinformatic, sequence analysis, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_15696, biotools:biopp | https://sources.debian.org/src/bppsuite/, https://groups.google.com/forum/#!categories/biopp-help-forum/all-questions, https://github.com/BioPP, https://bio.tools/biopp, | SCR_016055 | Bppsuite, Bppphyview, Bio++ program suite, Bio++ Phylogenetic Viewer | 2026-09-12 12:58:34 | 65 | |||||||
|
EnrichmentMap Resource Report Resource Website 500+ mentions |
EnrichmentMap (RRID:SCR_016052) | data processing software, data visualization software, software application, software resource, source code | Source code of a Cytoscape plugin for functional enrichment visualization. It organizes gene-sets, such as pathways and Gene Ontology terms, into a network to reveal which mutually overlapping gene-sets cluster together. | cytoscape, functional, visualization, enrichment, gene, mapping, genome, pathway, network, cluster, bio.tools |
is listed by: Debian is listed by: bio.tools is a plug in for: Cytoscape |
Canada Foundation for Innovation ; Heart and Stroke Foundation of Canada ; NHGRI P41 HG04118; Ontario Genomics Institute ; Ontario Research Fund (ORF) |
PMID:21085593 | biotools:enrichmentmap | https://github.com/BaderLab/EnrichmentMapApp, https://bio.tools/enrichmentmap | SCR_016052 | 2026-09-12 12:58:34 | 590 | |||||||
|
HyPhy Resource Report Resource Website 1000+ mentions |
HyPhy (RRID:SCR_016162) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning. | analysis, genetic, sequence, multiply, alignment, rate, pattern, data, evolution, platform, python, r, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NIGMS R01 ; NIH R01 AI47745; NIH U01 AI43638; NSF DBI-0096033; NSF DEB-9996118; University of California Universitywide AIDS Research Program IS02-SD-701; University of California ; San Diego Center for AIDS Research/NIAID Developmental Award 2 P30 AI36214 |
PMID:15509596 | Free, Available for download, Freely available | SCR_016271, biotools:HyPhy, OMICS_04235 | https://sources.debian.org/src/hyphy-pt/, https://veg.github.io/hyphy-site/, https://github.com/veg/hyphy, https://bio.tools/HyPhy, | SCR_016162 | HyPhy:Hypothesis Testing using Phylogenies, Hyphy-pt | 2026-09-12 12:58:36 | 1586 | |||||
|
zUMIs Resource Report Resource Website 100+ mentions |
zUMIs (RRID:SCR_016139) | data analysis software, data processing software, software application, software resource | Software pipeline to process RNA-seq data with UMIs. The input to this pipeline is paired-end fastq files, where one read contains the cDNA sequence and the other read contains UMI and Cell Barcode information. | single-cell, RNA-seq, UMI, Genomics, shell, r, perl, rna, cdna, cell, sequencing, bio.tools |
is listed by: bio.tools is listed by: Debian |
DOI:10.1101/153940 | Open source, Free, Available for download | biotools:zumis | https://bio.tools/zumis | SCR_016139 | zumi | 2026-09-12 12:58:35 | 128 | ||||||
|
Fastml Resource Report Resource Website 100+ mentions |
Fastml (RRID:SCR_016092) | data access protocol, software resource, web application, web service | Web application for the reconstruction of ancestral sequences. It computes maximum likelihood ancestral sequence reconstruction based on the phylogenetic relations between homologous sequences. | ancestral, amino-acid, sequence, reconstruction, phylogenetic, relation, accurate, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Bioinformatics Center at Tel-Aviv University ; Israel Science Foundation 878/09 |
PMID:22661579 | Free, Freely available | biotools:fastml, OMICS_08650 | https://bio.tools/fastml, https://sources.debian.org/src/fastml/ | SCR_016092 | The FastML Server | 2026-09-12 12:58:35 | 111 | |||||
|
BioPlex Resource Report Resource Website 1000+ mentions |
BioPlex (RRID:SCR_016144) | data or information resource, data repository, database, service resource, storage service resource | Database of cell lines with each expressing a tagged version of a protein from the ORFeome collection. The overarching project goal is to determine protein interactions for every member of the collection. | cell, line, protein, immunopurification, mass, spectrometry, interaction, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Harvard Medical School; Massachusetts; USA |
Canadian Institutes for Health Research ; NHGRI U41HG006673; NIDDK K01 DK098285 |
PMID:28514442 | biotools:bioplex_2.0 | https://bio.tools/bioplex_2.0 | SCR_016144 | BioPlex (biophysical interactions of ORFeome-based complexes), Harvard BioPlex, Biophysical Interactions of Orfeome-based comPLEXes (BioPLEX) | 2026-09-12 12:58:35 | 1378 | ||||||
|
mentha Resource Report Resource Website 100+ mentions |
mentha (RRID:SCR_016148) | data analysis software, data or information resource, data processing software, database, software application, software resource, web application | Software that archives evidence collected from different sources, then analyzes and presents these data. Its data come from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. | protein, ppi, imex, interactome, archival, bio.tools, FASEB list |
uses: PSICQUIC Registry is listed by: Debian is listed by: bio.tools is related to: IMEx - The International Molecular Exchange Consortium |
PMID:23900247 | biotools:mentha, r3d100011124 | https://bio.tools/mentha, https://doi.org/10.17616/R3SP8V | SCR_016148 | 2026-09-12 12:58:36 | 156 | ||||||||
|
Necklace Resource Report Resource Website 1+ mentions |
Necklace (RRID:SCR_016103) | alignment software, data processing software, image analysis software, software application, software resource | Software that combines reference and assembled transcriptomes for RNA-Seq analysis. It replaces many manual steps in the pipeline of RNA-Seq analyses involving species with incomplete genome or annotations. | RNA, Transcriptome, Non-model species, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:28836999 | Free, Available for download | biotools:necklace | https://bio.tools/necklace | SCR_016103 | Lace software | 2026-09-12 12:58:35 | 3 | ||||||
|
BLINK Resource Report Resource Website 1+ mentions |
BLINK (RRID:SCR_016288) | algorithm resource, data analysis software, data processing software, software application, software resource | Software for next level of genome wide association studies with both individuals and markers in millions. The method releases the requirement that causative genes are evenly distributed on genome and consequently boosts statistical power. | GWAS, SNP, dataset, r, genome, bayesian, linkage, nested, keyway, statistic, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Tutorial available | biotools:BLINK | https://bio.tools/BLINK | SCR_016288 | BLINK (Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway) | 2026-09-12 12:58:37 | 2 | |||||||
|
MetaCyto Resource Report Resource Website 1+ mentions |
MetaCyto (RRID:SCR_016415) | data analysis software, data processing software, software application, software resource, software toolkit | Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database. | automated, analysis, meta, flow, cytometry, data, bio.tools |
is listed by: Bioconductor is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: The Immunology Database and Analysis Portal (ImmPort) |
the National Institute of Allergy and Infectious Diseases HHSN272201200028C | Free, Available for download, Freely available | biotools:metacyto | https://bio.tools/metacyto | SCR_016415 | 2026-09-12 12:58:39 | 5 | |||||||
|
SMAGEXP Resource Report Resource Website 1+ mentions |
SMAGEXP (RRID:SCR_016360) | SMAGEXP | data analysis software, data processing software, software application, software resource, software toolkit | Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more. | transcriptomics, data, meta, analysis, MicroArrays, RNA-Seq, Galaxy, gene, expression, next, generation, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: Gene Expression Omnibus is related to: metaMA is related to: metaRNASeq |
PMID:30698691 | Free, Available for download, Freely available | biotools:SMAGEXP | https://bio.tools/SMAGEXP | SCR_016360 | Statistical Meta Analysis for Gene EXPression | 2026-09-12 12:58:38 | 2 | |||||
|
FluxModeCalculator Resource Report Resource Website 1+ mentions |
FluxModeCalculator (RRID:SCR_016290) | data analysis software, data processing software, software application, software resource | Software for performing flux mode analysis in stoichiometric models. FluxModeCalculator enables large-scale elementary flux mode (EFM) computation and uses the OpenMP API to optimally exploit processor architectures with multiple cores., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | efm, flux, stoichiometry, algorithm, matlab, linux, model, magnitude, bio.tools |
is listed by: Debian is listed by: bio.tools |
Biobanking and Biomolecular Resources Research Infrastructure (BBMRI) ; CardioVascular Research Netherlands (CVON-ENERGISE) ; Center of Medical Systems Biology (CMSB) ; European Network for Genetic and Genomic Epidemiology (ENGAGE) ; Netherlands Consortium for Systems Biology (NCSB) |
PMID:26685305 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fluxmodecalculator, OMICS_10894 | https://bio.tools/fluxmodecalculator | SCR_016290 | Flux Mode Calculator | 2026-09-12 12:58:37 | 1 | |||||
|
Lifebit Deploit Resource Report Resource Website 1+ mentions |
Lifebit Deploit (RRID:SCR_016428) | analysis service resource, data analysis service, data management software, production service resource, service resource, software application, software resource | Platform for computing management for data analysis on the cloud from the Lifebit company. Allows the computational analyses to be permanently linked to live analyses pipelines. | Lifebit, compute, management, data, analysis, cloud, integrate, data, reproduce, transparent, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:28398311 | Commercially available | biotools:nextflow | https://bio.tools/nextflow | SCR_016428 | 2026-09-12 12:58:39 | 2 | |||||||
|
Microscopy Image Browser Resource Report Resource Website 100+ mentions |
Microscopy Image Browser (RRID:SCR_016560) | MIB | data analysis software, data processing software, data visualization software, image processing software, software application, software resource, standalone software | Software package for advanced image processing, analysis, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets. | segmentation, analysis, multidimentional, dataset, light, electron, microscopy, image, processing, visualization, data, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: MATLAB |
Biocenter Finland ; Biological Imaging Network Academy of Finland ; University of Helsinki |
PMID:26727152 | Free, Available for download, Freely available | biotools:mib | https://www.youtube.com/watch?v=I9FWmJX_nl0&index=1&list=PLGkFvW985wz8cj8CWmXOFkXpvoX_HwXzj, https://bio.tools/mib | SCR_016560 | MIB, Microscopy Image Browser | 2026-09-12 12:58:41 | 160 | ||||
|
SPEX2 Resource Report Resource Website 1+ mentions |
SPEX2 (RRID:SCR_014923) | data analysis software, data processing software, sequence analysis software, software application, software resource | Automatic software program for profiling spatial gene expression patterns from Fly embryo ISH images. It utilizes image-based genome-scale profiling of whole-body mRNA patterns. | software, spatial gene expression, fly, embryo, extraction, mrna, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Carnegie Mellon University; Pennsylvania; USA |
PMID:20529936 | biotools:spex2 | https://bio.tools/spex2 | SCR_014923 | 2026-09-12 12:58:23 | 1 | ||||||||
|
DOGMA Resource Report Resource Website 100+ mentions |
DOGMA (RRID:SCR_015060) | software resource, web application | Web-based annotation tool for plant chloroplasts and animal mitochondrial genomes. DOGMA allows the use of BLAST searches against a custom database, and conservation of basepairing in the secondary structure of animal mitochondrial tRNAs to identify and annotate genes. | chloroplast, mitochondria, genome annotation, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
PMID:15180927 | Freely available | biotools:DOGMA | https://bio.tools/DOGMA | SCR_015060 | Dual Organellar GenoMe Annotator, Dual Organellar GenoMe Annotator (DOGMA) | 2026-09-12 12:58:25 | 428 | ||||||
|
Online Resource for Community Annotation of Eukaryotes Resource Report Resource Website 10+ mentions |
Online Resource for Community Annotation of Eukaryotes (RRID:SCR_014989) | OrcAE, ORCAE | data or information resource, narrative resource, wiki | Online genome annotation tool for validating and correcting gene annotations. OrcAE is community-driven and can be edited by account-holders in the research community. | genome annotation, gene validation, community driven, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Bioinformatics Gent has parent organization: Ghent University; Ghent; Belgium has parent organization: VIB; Flanders; Belgium |
PMID:23132114 | Free, Account required, The research community can contribute to this resource | biotools:orcae | https://bio.tools/orcae | SCR_014989 | Online Resource for Community Annotation of Eukaryotes (OrcAE) | 2026-09-12 12:58:24 | 17 | |||||
|
SeaView Resource Report Resource Website 1000+ mentions |
SeaView (RRID:SCR_015059) | data analysis software, data processing software, data visualization software, sequence analysis software, software application, software resource | Graphical user interface for multiple sequence alignment and molecular phylogeny. SeaView also generates phylogenetic trees. | sequence alignment, molecular phylogeny, phylogenetic tree, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
PMID:19854763 DOI:10.1093/molbev/msp259 |
Free, Available for download | OMICS_08908, biotools:seaview | https://bio.tools/seaview, https://sources.debian.org/src/seaview/ | SCR_015059 | 2026-09-12 12:58:25 | 1817 | |||||||
|
MeroX Resource Report Resource Website 50+ mentions |
MeroX (RRID:SCR_014956) | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Software tool for the analysis of cross-linking/mass spectrometry datasets using MS-cleavable cross-linkers. MeroX is specialized for MS/MS-cleavable cross linking reagents and identifies the specific fragmentation products of the cleavable cross links. | sequence analysis software, cross linking, mass spectrometry, MS cleavage, fragmentation, cleavable cross link, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: StavroX |
PMID:25261217 | THIS RESOURCE IS NO LONGER IN SERVICE | BioTools:MeroX, biotools:MeroX | https://bio.tools/MeroX, https://bio.tools/MeroX, https://bio.tools/MeroX | SCR_014956 | 2026-09-12 12:58:23 | 74 |
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.
