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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Recombination Detection Program Resource Report Resource Website 500+ mentions |
Recombination Detection Program (RRID:SCR_018537) | RDP | data analysis software, data processing software, software application, software resource | Software package to analyse nucleotide sequence data and identify evidence of genetic recombination. RDP3 is version of RDP program for characterizing recombination events in DNA-sequence alignments. RDP4 is version of RDP program for detection and analysis of recombination patterns in virus genomes. | DNA sequence, alignment, phylogenetic tree, nucleotide analysis, sequence data analysis, genetic recombination identification, DNA sequence alignment, recombinant pattern analysis, virus genome | Carnergie Corporation ; European Research Council ; Fund for Scientific Research Flanders ; NIAID AI090970; NIAID AI100665; NIGMS U01 GM110749; Polyomielitis Research Foundation ; South African Centre of High Performance Computing ; South African National Research Foundation ; Spanish Ministry of Science and Education ; University of Cape Town ; Wellcome Trust |
PMID:27774277 PMID:20798170 |
Free, Available for download, Freely available | SCR_018537 | Recombination Detection Program, RDP4, RDP3 | 2026-09-19 12:53:53 | 507 | |||||||
|
Tracer Resource Report Resource Website 1000+ mentions |
Tracer (RRID:SCR_019121) | data analysis software, data processing software, data visualization software, software application, software resource | Open source software tool for analysing trace files generated by Bayesian MCMC runs. Software package for visualising and analysing MCMC trace files generated through Bayesian phylogenetic inference. Provides kernel density estimation, multivariate visualisation, demographic trajectory reconstruction, conditional posterior distribution summary and more. | Analysing trace files, files generated by Bayesian MCMC runs, MCMC trace files, conditional posterior distribution summary, demographic trajectory reconstruction, Bayesian phylogenetic inference, kernel density estimation, multivariate visualisation | European Union Seventh Framework Programme ; NIAID R01 AI107034; NIAID U19 AI135995; NSF DMS 1264153; Wellcome Trust |
PMID:29718447 | Free, Available for download, Freely available | https://github.com/beast-dev/tracer, http://gensoft.pasteur.fr/docs/Tracer/v1.6, http://beast.community/tracer, https://github.com/beast-dev/tracer/releases/tag/v1.7.1 | SCR_019121 | Tracer v1.7.1, Tracer v1.6 | 2026-09-19 12:54:03 | 1598 | |||||||
|
Roary Resource Report Resource Website 500+ mentions |
Roary (RRID:SCR_018172) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for rapid large scale prokaryote pan genome analysis. Builds large scale pan genomes, identifying core and accessory genes. Makes construction of pan genome of thousands of prokaryote samples on standard desktop without compromising on accuracy of results. Not intended for meta genomics or for comparing extremely diverse sets of genomes. | Genome analysis, prokaryote pan genome, pan genome, gene identification, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools works with: Scoary |
Wellcome Trust | PMID:26198102 | Free, Available for download, Freely available | OMICS_09491, biotools:roary | https://github.com/sanger-pathogens/Roary, https://bio.tools/roary, https://sources.debian.org/src/roary/ | SCR_018172 | 2026-09-19 12:55:17 | 710 | ||||||
|
ClonalOrigin Resource Report Resource Website 1+ mentions |
ClonalOrigin (RRID:SCR_016061) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package for comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry. | comparative, analysis, sequence, bacteria, genome, reconstruct, recombination, events, ancestry, bayesian |
is listed by: Debian is listed by: OMICtools is related to: Imperial College London; London; United Kingdom is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
National Science Foundation DBI-0630765; Science Foundation of Ireland 05/FE1/B882; Wellcome Trust WT082930MA |
PMID:20923983 DOI:10.1534/genetics.110.120121 |
Free, Available for download | OMICS_18881 | https://sources.debian.org/src/clonalorigin/ | SCR_016061 | 2026-09-19 12:55:15 | 8 | ||||||
|
mRnd Resource Report Resource Website 100+ mentions |
mRnd (RRID:SCR_022156) | data access protocol, software resource, web service | Web tool for calculations for Mendelian Randomization. Power calculations for Mendelian Randomization. Used to calculate statistical power for Mendelian Randomization study, using Non Centrality Parameter based approach. | calculations for Mendelian Randomization, Mendelian Randomization, calculate statistical power, Mendelian Randomization study, Non Centrality Parameter | Australian National Health and Medical Research Council ; EU 7th Framework Programme ; Leducq Foundation ; Wellcome Trust |
PMID:24159078 | Free, Freely available | https://github.com/kn3in/mRnd | SCR_022156 | 2026-09-19 12:55:02 | 364 | ||||||||
|
BioMart Project Resource Report Resource Website 100+ mentions |
BioMart Project (RRID:SCR_002987) | data access protocol, data or information resource, portal, project portal, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Platform provides free software and data services to international scientific community in order to foster scientific collaboration and facilitate scientific discovery process. Project adheres to open source philosophy that promotes collaboration and code reuse. | biology, data, management, data mining, search, descriptive, graphical, application, perl, java, gold standard |
is used by: Blueprint Epigenome is related to: Mouse Genome Informatics (MGI) is related to: biomaRt has parent organization: Ontario Institute for Cancer Research has parent organization: European Bioinformatics Institute |
Breast Cancer Campaign Tissue Bank ; Center for Genome Regulation ; Center for Mathematical Modelling ; European Molecular Biology Laboratory ; NSF NRF 2013M3A6A4043695; Sandra Ibarra Foundation for Cancer ; Spanish Government ; U.S. Department of Energy ; Wellcome Trust |
PMID:21930506 PMID:19144180 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30184 | SCR_002987 | BioMart software | 2026-09-19 12:55:06 | 295 | ||||||
|
Seq-Gen Resource Report Resource Website 100+ mentions |
Seq-Gen (RRID:SCR_014934) | simulation software, software application, software resource | Software program that simulates the evolution of nucleotide or amino acid sequences along a phylogeny using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. | simulator, simulation software, molecular evolution, nucleotide, amino acid, sequence, phylogeny, phylogenetic tree |
is listed by: Debian is listed by: OMICtools has parent organization: University of Edinburgh; Scotland; United Kingdom |
Wellcome Trust ; BBSRC ; Fogarty ; The Royal Society |
DOI:10.1093/bioinformatics/13.3.235 | Available for download | OMICS_15373 | https://sources.debian.org/src/seq-gen/ | SCR_014934 | 2026-09-19 12:53:04 | 158 | ||||||
|
GENCODE Resource Report Resource Website 5000+ mentions Rating or validation data |
GENCODE (RRID:SCR_014966) | data or information resource, dataset, portal, project portal | Human and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation. | human, mouse, genome, annotation, sequence, gene features, bio.tools |
is listed by: Debian is listed by: bio.tools is affiliated with: ENCODE |
NHGRI 5U54HG004555; Wellcome Trust WT098051 |
PMID:22955987 | Free | biotools:GENCODE | https://bio.tools/GENCODE | SCR_014966 | ENCODE | 2026-09-19 12:56:04 | 8811 | |||||
|
Ariba Resource Report Resource Website 100+ mentions |
Ariba (RRID:SCR_015976) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Analysis software that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling. | software, analysis, tool, sequence, antibiotic, resistance, assembly, local, mlst |
is listed by: Debian is listed by: OMICtools |
Biotechnology and Biological Sciences Research Council BB/M014088/1; Wellcome Trust 206194 |
PMID:29177089 DOI:10.1099/mgen.0.000131 |
Free, Available for download, Freely available | OMICS_17327 | https://sources.debian.org/src/artemis/ | SCR_015976 | 2026-09-19 12:53:15 | 220 | ||||||
|
HumanNet Resource Report Resource Website 100+ mentions |
HumanNet (RRID:SCR_016146) | data analysis software, data or information resource, data processing software, database, software application, software resource, web application | Database of human protein-encoding genes that is constructed by a modified Bayesian integration of 'omics' data from multiple organisms. Each data type is weighted according to how well it links genes that are known to function together in humans, and each interaction has an associated log-likelihood score (LLS) that measures the probability of an interaction representing a true functional linkage between two genes. | probability, gene, protein, encode, statistic, likelihood, network, bayesian, omic, pathway, guilt by association, FASEB list |
has parent organization: University of Texas at Austin; Texas; USA has parent organization: Yonsei University; Seoul; South Korea |
Korean government (MEST) 2010-0017649; National Research Foundation of Korea (NRF) ; Packard Foundations ; POSCO TJ ; U.S. Army Research 58343-MA; Welch F1515; Wellcome Trust 076113; Wellcome Trust 085475 |
Freely available | SCR_016146 | 2026-09-19 12:53:18 | 135 | |||||||||
|
Research Data Management Platform Resource Report Resource Website 1+ mentions |
Research Data Management Platform (RRID:SCR_016268) | RDMP | data management software, data or information resource, data repository, service resource, software application, software resource, software toolkit, storage service resource | Software toolkit which automates the loading, storage, linkage and provision of data sets. It also cleans, transforms and documents provenance meta-data and domain knowledge to make data sets “research ready”. | metadata, reproducibility, anonymization, security, audit, clinical, dataset, translational, research, data, management, catalogue, health, informatics, linkage | has parent organization: University of Dundee; Scotland; United Kingdom | EU Horizon 2020 633983; Medical Research Council (MRC) MR/M501633/1; Wellcome Trust WT086113 |
Free, Available for download | https://hic.dundee.ac.uk/Installers/RDMP/Stable/ | SCR_016268 | 2026-09-19 12:53:20 | 2 | |||||||
|
Gaussian-Copula Mutual Information (GCMI) Resource Report Resource Website 10+ mentions |
Gaussian-Copula Mutual Information (GCMI) (RRID:SCR_016450) | GCMI | data analysis software, data processing software, software application, software resource | Software package of functions for calculating mutual information and other information theoretic quantities using a parametric Gaussian copula. | gaussian, copula, parametric, equation, calculation, python, matlab, repository, statistic | European Research Council 646657; UK Biotechnology and Biological Sciences Research Council (BBSRC) BB/D01400X1; UK Biotechnology and Biological Sciences Research Council (BBSRC) BB/J018929/1; UK Biotechnology and Biological Sciences Research Council (BBSRC) BB/L027534/1; UK Biotechnology and Biological Sciences Research Council (BBSRC) BB/M009742/1; Wellcome Trust 098433; Wellcome Trust 107802 |
Free, Available for download | SCR_016450 | gcmi : Gaussian-Copula Mutual Information, Gaussian-Copula Mutual Information | 2026-09-19 12:53:23 | 11 | ||||||||
|
GeneDB Gmorsitans Resource Report Resource Website 1+ mentions |
GeneDB Gmorsitans (RRID:SCR_004310) | GeneDB Gmorsitans, GeneDB G. morsitans | data or information resource, database | As of 12th March 2009, GeneDB provides access to the transcriptome of the Tsetse fly Glossina morsitans morsitans, the biological vector of African trypanosomiases. The current data set includes: >>7,015 contigs comprised of ESTs from Trypanosoma brucei infected midgut tissue (Lehane et al, Genome Biol. 2003;4(10):R63) >>7,493 contigs comprised of ESTs from salivary gland tissue >>18,404 contigs comprised of EST pooled from a range of different tissue- and developmental stage-specific libraries: head (2,700 ESTs), midgut (21,662 ESTs), reproductive organs (3, 438 ESTs), salivary gland (27,426 ESTs), larvae (2,304 ESTs), pupae (2,304 ESTs), fatbody (20,257 ESTs) (Attardo et al, Insect Molecular Biology 2006, 15(4):411-424), male and female whole bodies (19,968 ESTs). These data include the midgut and salivary gland ESTs used in the library specific clustering for the contig sets listed above. Initial automated annotations of product descriptions were manually revised by participants in two community annotation jamborees held under the auspice of the International Glossina Genome Initiative (IGGI) with funding by TDR. A Glossina morsitans morsitans genome project is currently also underway. To date, 2.4M capillary shotgun reads have been produced and the initial assembly is available to download via the ftp server and for blast analysis. | has parent organization: GeneDB | Wellcome Trust ; TDR |
nlx_32209 | SCR_004310 | Glossina morsitans GeneDB | 2026-09-19 12:56:43 | 2 | ||||||||
|
SUPFAM Resource Report Resource Website 10+ mentions |
SUPFAM (RRID:SCR_005304) | SUPFAM | data or information resource, database | SUPFAM is a database that consists of clusters of potentially related homologous protein domain families, with and without three-dimensional structural information, forming superfamilies. The present release (Release 3.0) of SUPFAM uses homologous families in Pfam (Version 23.0) and SCOP (Release 1.69) which are examples of sequence -alignment and structure classification databases respectively. The two steps involved in setting up of SUPFAM database are * Relating Pfam and SCOP families using a new profile-profile alignment algorithm AlignHUSH. This results in identifying many Pfam families which could be related to a family or superfamily of known structural information. * An all-against-all match among Pfam families with yet unknown structure resulting in identification of related Pfam families forming new potential superfamilies. The SUPFAM database can be used in either the Browse mode or Search mode. In Browse mode you can browse through the Superfamilies, Pfam families or SCOP families. In each of these modes you will be presented with a full list which can be easily browsed. In Search mode, you can search for Pfam families, SCOP families or Superfamilies based on keywords or SCOP/Pfam identifiers of families and superfamilies., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | duf/upf connections, 3-d structure, alignment, amino acid sequence, bioinformatics, clustering, homologous protein family, multiple sequence alignment, nmr, pali, pfam, phylogeny, protein classification, protein domain database, protein families, protein sequence database, rps_blast, scop, structural genomics, structure determination, superfamily, three-dimensional, x-ray crystalography |
is related to: Pfam is related to: SCOP: Structural Classification of Proteins has parent organization: Indian Institute of Science; Bangalore; India |
Council of Scientific and Industrial Research New Delhi ; Wellcome Trust |
PMID:15113407 PMID:11752317 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03517 | http://pauling.mbu.iisc.ernet.in/~supfam | SCR_005304 | 2026-09-19 12:56:50 | 13 | |||||
|
Major depressive disorder neuroimaging database Resource Report Resource Website 1+ mentions |
Major depressive disorder neuroimaging database (RRID:SCR_005835) | MaND | data or information resource, database | The Major Depressive Disorder Neuroimaging Database (MaND) contains information of 225 studies which have investigated brain structure (using MRI and CT scans) in patients with major depressive disorder compared to a control group. 143 studies and 63 brain structures are included in the meta-analysis. The database and meta-analysis are contained in an Excel spreadsheet file which may be freely downloaded from this website. | mri, brain, ct, neuroimaging, image, normal control | has parent organization: King's College London; London; United Kingdom | Major depressive disorder | Wellcome Trust ; National Institute for Health Research ; EPSRC |
PMID:21727252 | nlx_149353 | SCR_005835 | Major Depressive Disorder Neuroimaging Database (MaND) | 2026-09-19 12:56:54 | 2 | |||||
|
Retinal wave repository Resource Report Resource Website |
Retinal wave repository (RRID:SCR_010462) | Retinal wave repository | data or information resource, data set | A subset of the CARMEN repository, a curated set of data and code of multielectrode array recordings of spontaneous activity in developing mouse and ferret retina. The data have been annotated with minimal metadata and converted into HDF5 (Hierarchical data format, version 5) including the essential features of the recordings, such as developmental age, and genotype. All code and tools used in the analyses are also fully available for reuse, giving the ability to regenerate each figure and table and know exactly how the results were calculated, adding confidence in the research output and allowing others to easily build upon previous work. The addition of published data to the repository is encouraged. | hdf5, development, neural circuit, retina, eye, multielectrode, array recording, spontaneous activity, reproducible research, retinal wave, electrophysiology, multielectrode array, developmental age, genotype |
has parent organization: GigaScience has parent organization: Code Analysis Repository and Modelling for e-Neuroscience has parent organization: University of Cambridge; Cambridge; United Kingdom |
Developing retina, Aging | EPSRC EP/E002331/1; BBSRC BB/H023577/1; BBSRC BB/I000984/1; Wellcome Trust 083205/B/07/Z |
PMID:24666584 | Registration required, (CARMEN), Acknowledgement required, The community can contribute to this resource | nlx_157664 | http://www.damtp.cam.ac.uk/user/eglen/waverepo/ | SCR_010462 | A data repository and analysis framework for spontaneous neural activity recordings in developing retina | 2026-09-19 12:58:56 | 0 | |||
|
Africa Centre for Health and Population Studies Resource Report Resource Website 1+ mentions |
Africa Centre for Health and Population Studies (RRID:SCR_008964) | Africa Centre Datasets, Africa Center Datasets, AfricaCentre Datasets | data or information resource, data set | Longitudinal datasets of demographic, social, medical and economic information from a rural demographic in northern KwaZulu-Natal, South Africa where HIV prevalence is extremely high. The data may be filtered by demographics, years, or by individuals questionnaires. The datasets may be used by other researchers but the Africa Centre requests notification that anyone contact them when downloading their data. The datasets are provided in three formats: Stata11 .dta; tables in a MS-Access .accdb database; and worksheets in a MS-Excel .xlsx workbook. Datasets are generated approximately every six months containing information spanning the whole period of surveillance from 1/1/2000 to present. | medicine, hiv infection, economic, demography, biology, social, longitudinal |
is listed by: re3data.org is listed by: DataCite has parent organization: University of KwaZulu-Natal; Durban; South Africa |
HIV | Wellcome Trust ; Agence Nationale de Recherches sur le Sida et les Hepatites Virales ; Department for International Development ; USAID ; EDCTP ; South African MRC ; National Research Foundation ; CSIR ; UNFPA ; CIDA |
Open unspecified license, Data Use Agreement, Approval required | nlx_152006 | SCR_008964 | Africa Centre for Health and Population Studies Datasets, Africa Center for Health and Population Studies | 2026-09-19 12:58:41 | 4 | |||||
|
UK Biobank Resource Report Resource Website 1000+ mentions |
UK Biobank (RRID:SCR_012815) | biobank, material storage repository, service resource, storage service resource | Biobank provides data collected at Assessment Center and via online questionnaires on participants aged 40-69 years recruited throughout United Kingdom and provides summary information to improve prevention, diagnosis and treatment of serious and life threatening illnesses. | Data, collected, United Kingdom, prevention, diagnosis, treatment, illness, questionnaire, blood, urine, saliva, cognitive function, psychological status, hearing test, interview, operation, medication, blood pressure, body measurementdie |
is listed by: One Mind Biospecimen Bank Listing is related to: AstraZeneca PheWAS Portal |
cancer, heart diseases, stroke, diabetes, arthritis, osteoporosis, eye disorders, depression, dementia. | MRC ; Scottish Government ; UK Department of Health ; Wellcome Trust ; Welsh Assembly Government |
grid.421945.f, nlx_95741, ISNI: 0000 0004 0396 0496, Wikidata: Q7864819 | https://ror.org/02frzq211 | SCR_012815 | 2026-09-19 12:59:13 | 3905 | |||||||
|
University of Edinburgh Wellcome Trust Centre for Cell Biology Bioinformatics Core Facility Resource Report Resource Website |
University of Edinburgh Wellcome Trust Centre for Cell Biology Bioinformatics Core Facility (RRID:SCR_017151) | University of Edinburgh WTCCB Bioinformatics Core Facility | access service resource, core facility, service resource | Facility provides regular training sessions, tools, advice and data analysis services to Centre members. | core, facility, bioinformatics | has parent organization: University of Edinburgh; Scotland; United Kingdom | Wellcome Trust | Restricted | SCR_017151 | 2026-09-19 12:59:27 | 0 | ||||||||
|
Brain Intensity AbNormality Classification Algorithm Resource Report Resource Website 1+ mentions |
Brain Intensity AbNormality Classification Algorithm (RRID:SCR_024928) | BIANCA | data processing software, image analysis software, segmentation software, software application, software resource | Software tool for automated segmentation of white matter hyperintensities. Classifies image’s voxels based on their intensity and spatial features, and the output image represents the probability per voxel of being WMH. Flexible in terms of MRI modalities to use and offers different options for weighting spatial information, local spatial intensity averaging, and different options for choice of number and location of training points. | images voxels classification, automated segmentation of white matter hyperintensities, white matter hyperintensities, | is a plug in for: FSL | NIHR Oxford Biomedical Research Centre ; UK Stroke Association ; Wellcome Trust ; Wolfson Foundation |
PMID:27402600 | Free, Freely available | SCR_024928 | BIANKA:Brain Intensity AbNormality Classification Algorithm | 2026-09-19 01:00:09 | 7 |
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.
