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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Cumulus Resource Report Resource Website 1+ mentions |
Cumulus (RRID:SCR_021644) | data processing software, data analysis software, software resource, software application | Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data. | Single cell genomics, spatial transcriptomics, single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire, data |
uses: Pegasus uses: Cirrocumulus uses: Pegasus-fus is listed by: Terra is related to: BICCN has parent organization: Broad Institute |
Klarman Cell Observatory ; Manton Foundation ; HHMI ; Ludwig Center at MIT ; Leidos Biomedical Research ; Frederick National Laboratory for Cancer Research ; NCI |
DOI:10.1038/s41592-020-0905-x | Free, Available for download, Freely available | https://app.terra.bio/#workspaces/kco-tech/Cumulus, https://github.com/klarman-cell-observatory/cumulus/blob/91336094646217564a4f8e7b31c03c3c6bf2e84b/docs/index.rst | SCR_021644 | 2026-08-12 10:52:41 | 3 | |||||||
|
jcvi Resource Report Resource Website 10+ mentions |
jcvi (RRID:SCR_021641) | software library, software toolkit, software resource | Software tool as collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics. | Python libraries, parse bioinformatics files, assembly, annotation, comparative genomics | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/tanghaibao/jcvi/tree/v0.5.7, https://zenodo.org/record/31631#.YRaieYhKhPa | SCR_021641 | jcvi_PyPI, jcvi 1.1.17 | 2026-08-12 10:52:36 | 20 | ||||||||
|
TrainingSpace Resource Report Resource Website 1+ mentions |
TrainingSpace (RRID:SCR_022036) | data or information resource, online course, portal, training resource | Portal that provides multimedia educational content from courses, conference lectures, and laboratory exercises from some of leading neuroscience institutes and societies to be more accessible to global neuroscience community. | Training materials resource, neuroscience multimedia educational content, neuroscience community | Free, Freely available | SCR_022036 | 2026-08-12 10:52:49 | 1 | |||||||||||
|
PANC-DB Resource Report Resource Website 1+ mentions |
PANC-DB (RRID:SCR_021860) | data or information resource, topical portal, database, portal | Portal to make all Human Pancreas Analysis Program data available to anyone in research community and to interact with and connect scientific community. Stores clinical, molecular, cellular, immunology, imaging, and pathology data from pancreatic tissue and cell samples from organ donors with and without type 1 or type 2 diabetes. | HIRN, HPAP, Human Pancreas Analysis Program, |
is listed by: NIDDK Information Network (dkNET) is related to: Human Islet Research Network (HIRN) |
Free, Freely available | SCR_021860 | 2026-08-12 10:52:24 | 1 | ||||||||||
|
PaintOmics Resource Report Resource Website 10+ mentions |
PaintOmics (RRID:SCR_021859) | software resource, data access protocol, web service | Web tool for integrative visualization of multiple omic datasets onto KEGG pathways. Supports integrated visualization of multiple species of different biological kingdoms and offers user possibility to request any other organism present in KEGG database. | integrative visualization, multiple omic datasets, KEGG pathways, multiple species | Spanish Ministry of Science and Innovation ; GVA-FEDER |
DOI:10.1093/bioinformatics/btq594 PMID:29800320 |
Free, Freely available | SCR_021859 | PaintOmics 3, Paintomics | 2026-08-12 10:52:38 | 15 | ||||||||
|
SimulaBeta Resource Report Resource Website 1+ mentions |
SimulaBeta (RRID:SCR_021900) | simulation software, software resource, software application | Software tool as simulation program for insulin glucose feedback control. Based on nonlinear MiMe-NoCoDI model. | Open source, insulin, glucose, simulation, modelling, model, beta cell, homeostasis |
uses: CyberUnits is related to: SPINA Carb is related to: SimThyr has parent organization: Ruhr University Bochum; North Rhine-Westphalia; Germany has parent organization: Ulm University; Baden-Wurttemberg; Germany |
Deutsche Forschungsgemeinschaft (DFG) GRK 1041; Open Access Publication Funds of the Ruhr-Universität Bochum ; Germany ; Ministry of Education (MOE) Singapore |
PMID:36271244 | Free, Available for download, Freely available | DOI:10.5281/zenodo.4922800 | https://doi.org/10.5281/zenodo.4922800 | SCR_021900 | 2026-08-12 10:52:46 | 2 | ||||||
|
ANGSD Resource Report Resource Website 10+ mentions |
ANGSD (RRID:SCR_021865) | data processing software, data analysis software, software resource, software application | Software tool fo analysis of next generation sequencing data. Calculates various summary statistics, and performs association mapping and population genetic analyses utilizing full information in next generation sequencing data by working directly on raw sequencing data or by using genotype likelihoods. | analysing NGS data, next generation sequencing data analysis, raw sequencing data, genotype likelihoods | DOI:10.1186/s12859-014-0356-4 | Free, Available for download, Freely available | http://www.popgen.dk/angsd/index.php/ANGSD | SCR_021865 | Analysis of Next Generation Sequencing Data | 2026-08-12 10:52:38 | 47 | ||||||||
|
Platform for Epigenomic and Genomic Research Resource Report Resource Website 1+ mentions |
Platform for Epigenomic and Genomic Research (RRID:SCR_021861) | PEGR | software resource, data access protocol, web service | Web service platform logging metadata for genomic samples and high throughput sequencing, manages data processing workflows, and provides quality control reporting and visualization. PEGR links people, samples, protocols, sequencing and bioinformatics computation to comply with FAIR best practices for publications and data management plans.Tracks and quality controls experiments from conception to publication ready figures, compatible with multiple assays and bioinformatic pipelines. It supports rigor and reproducibility for biochemists working at wet bench, while continuing to fully support reproducibility and reliability for bioinformaticians through integration with Galaxy platform. | FAIR compliance, platform logging metadata, genomic samples, high throughput sequencing, experiments quality controls, tracking experiments, rigor and reproducibility support | DOI:10.1101/2021.07.26.453821 | Free, Available for download, Freely available | SCR_021861 | 2026-08-12 10:52:45 | 8 | |||||||||
|
granulator Resource Report Resource Website 1+ mentions |
granulator (RRID:SCR_022158) | data processing software, data analysis software, software resource, software application | Software R package for cell type deconvolution of heterogeneous tissues based on bulk RNAseq data or single cell RNAseq expression profiles.Provides unified testing interface to rapidly run and benchmark multiple deconvolution methods. | cell type deconvolution, heterogeneous tissues, RNAseq data, estimate cell type proportions, bulk transcriptomics data, unified testing interface | Free, Available for download, Freely available | https://github.com/xanibas/granulator | SCR_022158 | 2026-08-12 10:52:40 | 3 | ||||||||||
|
Motif Mutation Analysis for Regulatory Genomic Elements Resource Report Resource Website 500+ mentions |
Motif Mutation Analysis for Regulatory Genomic Elements (RRID:SCR_021902) | MMARGE | software toolkit, software application, data processing software, software resource, data analysis software | Software package that integrates genome wide genetic variation with epigenetic data to identify collaborative transcription factor pairs. Optimized to work with chromatin accessibility assays such as ATAC-seq or DNase I hypersensitivity, as well as transcription factor binding data collected by ChIP-seq. Used to identify combinations of cell type specific transcription factors while simultaneously interpreting functional effects of non-coding genetic variation. | genome wide genetic variation, epigenetic data, identify collaborative transcription factor pairs, interpreting functional effects, non-coding genetic variation | NCI CA173903; NIGMS GM085764; NIDDK DK091183; NHLBI R00 123485 |
PMID:29893919 | Free, Available for download, Freely available | SCR_021902 | 2026-08-12 10:52:38 | 608 | ||||||||
|
CancerMIRNome Resource Report Resource Website 10+ mentions |
CancerMIRNome (RRID:SCR_022092) | data or information resource, database, data access protocol, software resource, web service | Web server for cancer miRNome interactive analysis and visualization based on human miRNome data of cancer types from The Cancer Genome Atlas, and public cancer circulating miRNome profiling datasets from NCBI Gene Expression Omnibus and ArrayExpress. Comprehensive database for interactive analysis and visualization of miRNA expression profiles. | cancer miRNome interactive analysis, human miRNome data, cancer data, miRNA expression profiles |
is related to: The Cancer Genome Atlas is related to: ArrayExpress |
Riverside Faculty Start-up Fund ; UC Cancer Research Coordinating Committee Competition Award ; UC Academic Senate CoR Research Grant ; United States Department of Agriculture ; National Natural Science Foundation of China ; Science and Technology Project of Guizhou Province |
DOI:10.1093/nar/gkab784 | Free, Freely available | SCR_022092 | 2026-08-12 10:52:27 | 48 | ||||||||
|
CEU Mass Mediator Resource Report Resource Website 10+ mentions |
CEU Mass Mediator (RRID:SCR_022090) | CMM | software resource, data access protocol, web service | Software tool for searching metabolites in different databases including Kegg, HMDB, LipidMaps, Metlin, NP Atlas, KNApSAcK, MINE and in house library. Designed for searches through experimental masses obtained from mass spectrometry techniques. Metabolite annotation tool that uses expert system to score putative annotation based on analytical information acquired under different configurations. | Metabolite annotation, searching metabolites in different databases, experimental masses, mass spectrometry, | DOI:10.1016/j.jpba.2018.02.046 DOI:10.1021/acs.jproteome.8b00720 |
Free, Freely available | SCR_022090 | CEU Mass Mediator version 3.0, CMM 2.0, CMM 3.0, CEU Mass Mediator 2.0 | 2026-08-12 10:52:40 | 35 | ||||||||
|
Rcorrector Resource Report Resource Website 10+ mentions |
Rcorrector (RRID:SCR_022011) | data processing software, data analysis software, software resource, software application | Software tool as kmer based error correction method for RNAseq data. Can also be applied to other types of sequencing data where read coverage is nonuniform, such as single cell sequencing. Used for error correction for Illumina RNAseq reads. | RNA-seq, k-mer, random sequencing errors correction, kmer based error correction, RNA-seq data, sequencing data, nonuniform read coverage, Illumina RNAseq reads error correction | NSF ABI1159078; NSF ABI1356078 |
DOI:10.1186/s13742-015-0089-y | Free, Available for download, Freely available | SCR_022011 | RNA-seq error CORRECTOR | 2026-08-12 10:52:39 | 39 | ||||||||
|
Ruby on Rails Resource Report Resource Website 10+ mentions |
Ruby on Rails (RRID:SCR_022129) | RoR | software library, software toolkit, web application, software resource | Open source web application development framework. Model View Controller framework, providing default structures for database, web service, and web pages. | MVC, model–view–controller, web application development framework, Rails | DOI:10.1109/MS.2007.176 | Free, Available for download, Freely available | https://www.wikidata.org/wiki/Q190478 | https://github.com/rails/rails | SCR_022129 | 2026-08-12 10:52:51 | 10 | |||||||
|
Neuronanalyser Resource Report Resource Website 1+ mentions |
Neuronanalyser (RRID:SCR_022007) | 2d time-series analysis software, software application, data processing software, time-series analysis software, software resource, data analysis software | Software analysis toolkit for tracking blobs and extracting intensity values from imaging data, designed for use with ratiometric fluorescent sensors. | tracking blobs, extracting intensity values, imaging data, ratiometric fluorescent sensors | ERC - European Research Council 269058 | Free, Available for download, Freely available | SCR_022007 | 2026-08-12 10:52:26 | 3 | ||||||||||
|
PLUMED 2 Resource Report Resource Website 10+ mentions |
PLUMED 2 (RRID:SCR_021952) | software library, software toolkit, software resource | Open source, community developed library that provides range of different methods, which include enhanced sampling algorithms, free energy methods, tools to analyze vast amounts of data produced by molecular dynamics simulations. PLUMED 2 is complete rewrite of the code in object oriented programming language C plus plus. This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has simpler interface with the MD engines and provides single software library containing both tools and core facilities. | Molecular dynamics analysis, enhanced sampling algorithms, free energy methods, PLUMED | MIUR grant FIRB ; European Research Council ; Marie Curie Intra European Fellowship ; CeCAM ; SISSA |
DOI:10.1016/j.cpc.2013.09.018 | Free, Available for download, Freely available | www.plumed-code.org | SCR_021952 | PLUgin for MolEcular Dynamics 2 | 2026-08-12 10:52:25 | 34 | |||||||
|
StAMPP Resource Report Resource Website 1+ mentions |
StAMPP (RRID:SCR_022022) | data processing software, data analysis software, software resource, software application | Software R package for statistical analysis of mixed ploidy populations.Used for calculation of population structure and differentiation based on single nucleotide polymorphism genotype data from populations of any ploidy level, and/or mixed ploidy levels. | statistical analysis, mixed ploidy populations, single nucleotide polymorphism genotype data | is related to: R Project for Statistical Computing | Victorian Department of Primary Industries ; Geoffrey Gardiner Foundation ; Meat and Livestock Australia ; New Zealand Agriseeds ; Christchurch ; New Zealand ; Australian Postgraduate Award ; Dairy Futures CRC |
DOI:10.1111/1755-0998.12129 | Free, Available for download, Freely available | https://github.com/lpembleton/StAMPP | SCR_022022 | 2026-08-12 10:52:49 | 6 | |||||||
|
hierfstat Resource Report Resource Website 10+ mentions |
hierfstat (RRID:SCR_022021) | data processing software, data analysis software, software resource, software application | Software R package for estimation and tests of hierarchical F statistics.Used to estimate hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in hierarchy.Intended for analysis of population structure using genetic markers. | estimation and tests of hierarchical F statistics, haploid or diploid genetic data, analysis of population structure, genetic markers | DOI:10.1093/genetics/144.4.1933 DOI:10.1534/genetics.116.198424 |
Free, Available for download, Freely available | https://github.com/jgx65/hierfstat | SCR_022021 | 2026-08-12 10:52:26 | 11 | |||||||||
|
ZEN-ZEISS Efficient Navigation Resource Report Resource Website 100+ mentions |
ZEN-ZEISS Efficient Navigation (RRID:SCR_021725) | ZEN | data visualization software, data acquisition software, image processing software, software application, data processing software, software resource | Software package for ZEISS light microscopy systems. Universal user interface for every imaging system from ZEISS to assist to acquire images, process images, visualize big data by GPU powered 3D engine, analyze images via Machine Learning-based tools, correlate between light-light or light-electron microscopes, store raw data in secure format locally or in the cloud., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | ZEISS light microscopy, ZEISS, imaging | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_021725 | ZEN2010 B SP1 software, ZEISS Efficient Navigation, ZEN - ZEISS Efficient Navigation | 2026-08-12 10:52:37 | 145 | |||||||||
|
MutaRNA Resource Report Resource Website 1+ mentions |
MutaRNA (RRID:SCR_021723) | service resource, production service resource, analysis service resource, software resource, data access protocol, web service | Web server predicts and visualizes mutation induced structure changes of single nucleotide polymorphism in RNA sequence. This covers changes in accessibility (single strandedness) of molecule, its intra molecular base pairing potential and its base pairing probabilities. One of Freiburg RNA tools. | Mutation induced structure changes, single nucleotide polymorphism, RNA sequence | has parent organization: University of Freiburg; Baden-Wurttemberg; Germany | German Research Foundation ; Germany Excellence Strategy ; Baden-Wuerttemberg Ministry of Science ; Research and Art ; University of Freiburg |
PMID:32392303 | Free, Freely available | SCR_021723 | Mutational Analysis of RNAs | 2026-08-12 10:52:23 | 2 |
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.
