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https://www.ncbi.nlm.nih.gov/geo/
Functional genomics data repository supporting MIAME-compliant data submissions. Includes microarray-based experiments measuring the abundance of mRNA, genomic DNA, and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. Array- and sequence-based data are accepted. Collection of curated gene expression DataSets, as well as original Series and Platform records. The database can be searched using keywords, organism, DataSet type and authors. DataSet records contain additional resources including cluster tools and differential expression queries.
Proper citation: Gene Expression Omnibus (GEO) (RRID:SCR_005012) Copy
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Software package for analysis of brain imaging data sequences. Sequences can be a series of images from different cohorts, or time-series from same subject. Current release is designed for analysis of fMRI, PET, SPECT, EEG and MEG.
Proper citation: SPM (RRID:SCR_007037) Copy
http://harvester.fzk.de/harvester/
Harvester is a Web-based tool that bulk-collects bioinformatic data on human proteins from various databases and prediction servers. It is a meta search engine for gene and protein information. It searches 16 major databases and prediction servers and combines the results on pregenerated HTML pages. In this way Harvester can provide comprehensive gene-protein information from different servers in a convenient and fast manner. As full text meta search engine, similar to Google trade mark, Harvester allows screening of the whole genome proteome for current protein functions and predictions in a few seconds. With Harvester it is now possible to compare and check the quality of different database entries and prediction algorithms on a single page. Sponsors: This work has been supported by the BMBF with grants 01GR0101 and 01KW0013.
Proper citation: Bioinformatic Harvester IV (beta) at Karlsruhe Institute of Technology (RRID:SCR_008017) Copy
Seattle based independent, nonprofit medical research organization dedicated to accelerating the understanding of how human brain works. Provides free data and tools to researchers and educators and variety of unique online public resources for exploring the nervous system. Integrates gene expression data and neuroanatomy, along with data search and viewing tools, these resources are openly accessible via the Allen Brain Atlas data portal. Provides Allen Mouse Brain, Allen Spinal Cord Atlas, Allen Developing Mouse Brain Atlas, Allen Human Brain Atlas,Allen Mouse Brain Connectivity Atlas, Allen Cell Type Database, The Ivy Glioblastoma Atlas Project (Ivy GAP), The BrainSpan Atlas of the Developing Human Brain.
Proper citation: Allen Institute for Brain Science (RRID:SCR_006491) Copy
Site for collection and distribution of clinical data related to genetic analysis of drug abuse phenotypes. Anonymous data on family structure, age, sex, clinical status, and diagnosis, DNA samples and cell line cultures, and data derived from genotyping and other genetic analyses of these clinical data and biomaterials, are distributed to qualified researchers studying genetics of mental disorders and other complex diseases at recognized biomedical research facilities. Phenotypic and Genetic data will be made available to general public on release dates through distribution mechanisms specified on website.
Proper citation: National Institute on Drug Abuse Center for Genetic Studies (RRID:SCR_013061) Copy
https://github.com/NOCIONS/letswave6/wiki/Download-and-setup
Open source electroencephalogram (EEG) signal processing toolbox to process and visualise EEG/MEG data and other neurophysiological signals.
Proper citation: Letswave (RRID:SCR_016414) Copy
https://www.fil.ion.ucl.ac.uk/spm/ext/#TSDiffAna
Software tool developed for Statistical Parametric Mapping (SPM) that computes slicewise scan by scan difference and standard deviations. Used to examine quality of image timeseries.
Proper citation: TSDiffAna (RRID:SCR_016656) Copy
https://kidsfirstdrc.org/portal/portal-features/
Portal for analysis and interpretation of pediatric genomic and clinical data to advance personalized medicine for detection, therapy, and management of childhood cancer and structural birth defects. For patients, researchers, and clinicians to create centralized database of well curated clinical and genetic sequence data from patients with childhood cancer or structural birth defects.
Proper citation: Kids First Data Resource Portal (RRID:SCR_016493) Copy
Cloud based platform for simplified, standardized and reproducible microbiome data analysis. Allows users to process microbiome datasets through pipelines of existing software tools.
Proper citation: Nephele (RRID:SCR_016595) Copy
Software tool for a flow cytometry data analysis for Microsoft Windows enviroment developed by CyFlo Ltd. Has analysis capabilities, such as dot plot, histogram and statistics.
Proper citation: Cyflogic (RRID:SCR_016635) Copy
https://www.ncbi.nlm.nih.gov/sutils/pasc/viridty.cgi
Web tool for analysis of pairwise identity distribution within viral families. Used for virus sequence-based classification. Data in the system are updated every day to reflect changes in virus taxonomy and additions of new virus sequences to the public database.
Proper citation: PASC (RRID:SCR_016642) Copy
http://ccg.vital-it.ch/snp2tfbs
Collection of text files providing specific annotations for human single nucleotide polymorphisms (SNPs), namely whether they are predicted to abolish, create or change the affinity of one or several transcription factor (TF) binding sites. Used to investigate the molecular mechanisms underlying regulatory variation in the human genome. SNP2TFBS is also accessible over a web interface, enabling users to view the information provided for an individual SNP, to extract SNPs based on various search criteria, to annotate uploaded sets of SNPs or to display statistics about the frequencies of binding sites affected by selected SNPs.
Proper citation: SNP2TFBS (RRID:SCR_016885) Copy
Community based, biologist friendly web platform for creating and meta analyzing annotated gene expression data compendia., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: OMiCC (RRID:SCR_016604) Copy
https://cran.r-project.org/web/packages/factoextra/index.html
R package from CRAN to extract and visualize the results of multivariate data analysis.
Proper citation: factoextra (RRID:SCR_016692) Copy
https://github.com/ANGSD/ngsRelate
Software tool for estimating pairwise relatedness from next-generation sequencing data.
Proper citation: ngsRelate (RRID:SCR_016588) Copy
https://satijalab.org/seurat/get_started.html
Software as R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data.
Proper citation: Seurat (RRID:SCR_016341) Copy
Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.
Proper citation: Bioconductor (RRID:SCR_006442) Copy
http://dsarm.niapublications.org/
THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 18, 2014.
A networking site for investigators using animal models to study aging, developed to provide a venue for sharing information about research models for aging studies. If you have tissue or data from animal models relevant to aging research that you are willing to share with other investigators, D-SARM allows you to identify the model and provides a secure, blinded email contact for investigators who would like to contact you about acquiring tissue or related resources. Investigators looking for resources from a particular model enter search terms describing the model of interest and then use the provided link to send emails to the contacts (names blinded) listed in the search results to initiate dialog about tissue or resources available for sharing. The database is housed on a secure server and admission to the network is moderated by the NIA Project Officer and limited to investigators at academic, government and non-profit research institutions. The goal is to provide a secure environment for sharing information about models used in aging research, promoting the sharing of resources, facilitating new research on aging in model systems, and increasing the return on the investment in research models.
Proper citation: Database for Sharing Aging Research Models (RRID:SCR_008691) Copy
Ensembl SARS-Cov2 data portal.
Proper citation: Ensembl Covid-19 (RRID:SCR_024704) Copy
https://cab.spbu.ru/software/spades/
Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: SPAdes (RRID:SCR_000131) Copy
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