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https://github.com/AndreMacedo88/VEnCode
Software tool to perform intersectional genetics-related operations to find VEnCodes using databases provided by FANTOM5 consortium, namely CAGE enhancer and transcription start site (TSS) databases.
Proper citation: VEnCode (RRID:SCR_018024) Copy
https://biit.cs.ut.ee/gprofiler/page/r
Software R interface to g:Profiler. Uses publicly available APIs of g:Profiler web tool which ensures that results from all of interfaces are consistent. Used for gene list functional enrichment analysis and namespace conversion. gprofiler2 package supports all the same organisms, namespaces and data sources as the web tool.
Proper citation: gProfiler2 (RRID:SCR_018190) Copy
Web based serverless viewer of QIIME 2 artifacts and visualizations. Client side interface for viewing QIIME 2 artifacts and visualizations. Not needed working QIIME 2 installation to inspect QIIME 2 results. Supports viewing externally hosted files by automatically downloading and displaying them when links to files are provided.
Proper citation: QIIME 2 View (RRID:SCR_018074) Copy
http://circadb.hogeneschlab.org/
Database of mammalian circadian gene expression profiles. Works with link outs to Wikipedia, HomoloGene, Refseq, etc.. Open source database of circadian transcriptional profiles from time course expression experiments from mice and humans.
Proper citation: CircaDB (RRID:SCR_018078) Copy
http://www.milesculabs.org/QuB.html
Integrated software platform for ion channel biophysics and neurophysiology.Used to explore dynamics of hidden states in memoryless system. Open source software suite for solving kinetic models, for report generation with publishable graphics, function fitting and scripting for new and repeated processing and AD/DA I/O. Can be applied to any data modeled with Markov kinetics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: QuB (RRID:SCR_018076) Copy
Independent, non-profit organization that has developed global data-sharing and analytics platform to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through creation and implementation of sustainable global data-sharing enterprise. Our focus is on sharing individual participant-level data from completed clinical trials. Users can search listed studies, request data sets from data contributors, aggregate data, or share data of their own. Vivli (Center for Clinical Research Data) is launching a portal to share participant-level data from COVID trials.
Proper citation: Vivli (RRID:SCR_018080) Copy
Software package that autonomously diagnoses rare diseases from next generation sequencing NGS data using artificial intelligence by Diploid.
Proper citation: MOON (RRID:SCR_018005) Copy
Probabilistic programming language for specifying statistical models. Defines log probability function over parameters conditioned on specified data and constants. Platform for statistical modeling and high performance statistical computation. Provides full Bayesian inference for posterior expectations including parameter estimation and posterior predictive inference by defining appropriate derived quantities of interest.
Proper citation: Stan (RRID:SCR_018459) Copy
http://www.nitrc.org/projects/reprocontainers/
Software containerized environments for reproducible neuroimaging. Part of ReproNim - Center for Reproducible Neuroimaging Computation. DataLad dataset with collection of popular computational tools provided within ready to use containerized environments.
Proper citation: ReproNim/containers (RRID:SCR_018467) Copy
http://bioinformatics.fh-hagenberg.at/site/index.php?id=17
Software scoring system to identify peptides out of tandem mass spectrometry data using database of known proteins. Universal identification algorithm optimized for high resolution and high accuracy tandem mass spectra. Software tool as peptide and protein identification algorithm developed by Bioinformatics Research Group University of Applied Sciences Upper Austria in close cooperation with group of Karl Mechtler at IMP Vienna, Austria.
Proper citation: MS Amanda (RRID:SCR_018396) Copy
http://statistika.mfub.bg.ac.rs/interactive-dotplot/
Web-based tool to create customized interactive graphics, including univariate scatterplots, box plots, and violin plots, for comparing values of continuous variable across different study groups, visualization of subgroups or clusters of non-independent data. Web visualization tool for creating dot plots, box plots and violin plots for small sample size data sets.
Proper citation: Interactive Dotplot (RRID:SCR_018329) Copy
http://dambe.bio.uottawa.ca/DAMBE/dambe.aspx
Software package for data analysis in molecular biology and evolution. Integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data. Used for genomic and phylogenetic data analysis on Windows, Linux, and Macintosh computers.
Proper citation: DAMBE (RRID:SCR_018528) Copy
https://github.com/lmb-embrapa/machado
Software tool as framework to store, search and visualize biological data. Django instance provides data management, visualization, and searching functionalities to Chado databases. Resulting object-relational framework enables users, not only to set up local instance containing data regarding their organisms of interest, but also to develop all sorts of tools by accessing open source code.
Proper citation: Machado (RRID:SCR_018428) Copy
https://github.com/OHDSI/CohortMethod
Software R package for performing new user cohort studies in observational database in OMOP Common Data Model.
Proper citation: CohortMethod (RRID:SCR_018511) Copy
https://sedfitsedphat.nibib.nih.gov/software/default.aspx
Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly.
Proper citation: SEDFIT (RRID:SCR_018365) Copy
https://github.com/grecolab/TinderMIX
Software tool as framework for dose and time dependent gene expression analysis which aims to identify groups of genes that show dynamic dose response behaviour. Software R package to cluster gene expression by contour plots. Used to analyse toxicogenomics data with multiple dose levels and time points and to identify expression patterns with respect to both variables and to cluster molecular features.
Proper citation: TinderMIX (RRID:SCR_018364) Copy
http://gpcr.biocomp.unibo.it/predgpi/pred.htm
Prediction system for GPI-anchored proteins. Used to predict presence of GPI-anchor and position of omega site. Prediction server based on support vector machine for discrimination of anchoring signal, and on Hidden Markov Model for prediction of most probable omega site. Method for screening whole proteomes.
Proper citation: PredGPI (RRID:SCR_018363) Copy
http://staraniso.globalphasing.org/cgi-bin/staraniso.cgi
Web server for anisotropy of diffraction limit and Bayesian estimation of structure amplitudes by Global Phasing Limited. Server uses DEBYE and STARANISO software to perform anisotropic cut off of merged intensity data, to perform Bayesian estimation of structure amplitudes and to apply anisotropic correction to data.
Proper citation: STARANISO (RRID:SCR_018362) Copy
APID Interactomes (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). The interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.
Proper citation: Agile Protein Interactomes DataServer (RRID:SCR_008871) Copy
Platform for sharing data, with very large storage capability for electrophysiological data, EEG data is included. This service is provided for neuroscientists to facilitate data access, data storage, data analysis and data sharing. This service is developed and maintained by the German Node of the International Neuroinformatics Coordinating Facility. The global scale of neuroinformatics offers unprecedented opportunities for scientific collaborations between and among experimental and theoretical neuroscientists. To fully harvest these possibilities, coordinated activities are required to improve key ingredients of neuroscience: data access, data storage, and data analysis, together with supporting activities for teaching and training. Focusing on the development and free distribution of tools for handling and analyzing neurophysiological data, G-Node aims at addressing these aspects as part of the International Neuroinformatics Coordination Facility (INCF) and the German Bernstein Network for Computational Neuroscience (NNCN). G-Node also serves as an international forum for Computational Neuroscientists that are interested in sharing experimental data and tools for data analysis and modeling. G-Node is funded through the German Federal Ministry of Education and Research and hosted by Ludwig-Maximilians-Universit-Munchen.
Proper citation: G-node portal electrophysiology data sharing (RRID:SCR_008893) Copy
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