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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Driftage Resource Report Resource Website 1+ mentions |
Driftage (RRID:SCR_021031) | data processing software, software development tool, code testing framework, 2d time-series analysis software, software application, data analysis software, software resource, time-series analysis software, 1d time-series analysis software | Software tool as modular multi agent framework to detect concept drifts from batch or streaming data. | Concept Drift, Data Drift, Anomaly Detection, Time Series, Multi-agent Systems, detect concept drifts | Free, Available for download, Freely available | SCR_021031 | 2026-08-14 09:28:19 | 1 | |||||||||||
|
Electron Microscopy Public Image Archive Resource Report Resource Website 50+ mentions |
Electron Microscopy Public Image Archive (RRID:SCR_019237) | EMPIAR | data or information resource, storage service resource, service resource, data repository | Public archive for raw electron microscopy image data. Resource for raw 2D electron microscopy images. Used to browse, upload and download raw images to build 3D structure. Provides access to raw data to facilitate methods development and validation. Complements Electron Microscopy Data Bank where 3D volumes are stored, and uses Aspera platform for data transfers. | CryoEM, cryo electron microscopy, raw electron microscopy images, electron microscopy images, raw images, raw data, image data | UK Biotechnology and Biological Sciences Research Council | PMID:27067018 | Free,Freely available | SCR_019237 | 2026-08-14 09:28:28 | 83 | ||||||||
|
Program MARK Resource Report Resource Website 1+ mentions |
Program MARK (RRID:SCR_019281) | data processing software, software application, data analysis software, software resource | Software tool to provide parameter estimates from marked animals when they are re-encountered at later time, to create population size estimates. Used for analysis of data from marked individuals. | Parameter estimates, marked animal, marked animal data, re-encountered animals, population size estimates | has parent organization: Colorado State University; Colorado; USA | Free, Available for download, Freely available | SCR_019281 | 2026-08-14 09:28:07 | 4 | ||||||||||
|
SCIGA Resource Report Resource Website 10+ mentions |
SCIGA (RRID:SCR_021002) | software toolkit, data processing software, software application, data analysis software, software resource | Software Perl toolkit for 10X single cell immunoglobulin repertoires analysis. Uses raw reads or output of Cellranger as input and performs reads quality control, immunoglobulin sequence assembly, sequence annotation, heavy- and light- chain pairing, computing statistics and visualizing. | 10X single cell immunoglobulin repertoires analysis, quality control, immunoglobulin sequence assembly, sequence annotation, heavy and light chain pairing, computing statistics, visualizing. | Free, Available for download, Freely available | biotools:sciga | https://bio.tools/sciga | SCR_021002 | SCIGA_v1.0.0.tar.gz | 2026-08-14 09:28:18 | 10 | ||||||||
|
Flowlogic Resource Report Resource Website 50+ mentions |
Flowlogic (RRID:SCR_020942) | data processing software, software application, data analysis software, software resource | Software tool for flow cytometry data analysis by Miltenyi Biotec. | Flow cytometry data, data analysis, flow cytometry, Miltenyi Biotec | is listed by: SoftCite | Restricted | SCR_020942 | Flowlogic TM Software, Flowlogic Software | 2026-08-14 09:28:17 | 81 | |||||||||
|
BrainVision PyCorder Resource Report Resource Website 50+ mentions |
BrainVision PyCorder (RRID:SCR_019286) | data processing software, software application, software resource, data acquisition software | Open source acquisition program, based on Python programming language, for setting up BrainVision actiCHamp amplifier and storing data. | Acquision Python program, setting up actiCHamp amplifier, BrainVision | https://www.brainlatam.com/manufacturers/brain-products/pycorder-127 | SCR_019286 | PyCorder | 2026-08-14 09:28:08 | 55 | ||||||||||
|
SIMR Resource Report Resource Website 1+ mentions |
SIMR (RRID:SCR_019287) | software toolkit, data processing software, software application, data analysis software, software resource | Software R package for power analysis of generalized linear mixed models by simulation. Used to calculate power for generalised linear mixed models. | Power analysis, generalized linear mixed models, calculate power, simulation | is listed by: CRAN | New Zealand Ministry of Business ; Innovation and Employment |
DOI:10.1111/2041-210X.12504 | Free, Available for download, Freely available | https://github.com/pitakakariki/simr | SCR_019287 | simr, simR | 2026-08-14 09:28:28 | 4 | ||||||
|
CiteFuse Resource Report Resource Website 1+ mentions |
CiteFuse (RRID:SCR_019321) | data processing software, software application, data analysis software, software resource | Software R package consisting of suite of tools for doublet detection, modality integration, clustering, differential RNA and protein expression analysis, antibody-derived tag evaluation, ligand-receptor interaction analysis and interactive web-based visualization of CITE-seq data. | Data pre processing, modality integration, clustering, differential RNA, ADT, expression analysis, ADT evaluation, ligand receptor interaction analysis, CITE-seq data, cellular indexing of transcriptomes and epitopes by sequencing, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian has parent organization: University of Sydney; Sydney; Australia |
PMID:32353146 | Free, Available for download, Freely available | biotools:citefuse | https://bioconductor.org/packages/CiteFuse/, https://github.com/SydneyBioX/CiteFuse/, http://shiny.maths.usyd.edu.au/CiteFuse/, https://bio.tools/CiteFuse | SCR_019321 | Cellular Indexing of Transcriptomes and Epitopes Fuse, Cellular indexing of transcriptomes and epitopes Fuse | 2026-08-14 09:28:29 | 3 | ||||||
|
MP3 tool Resource Report Resource Website 1+ mentions |
MP3 tool (RRID:SCR_019282) | software application, simulation software, software resource | Software tool for prediction of pathogenic proteins in genomic and metagenomic data. Used for identification of partial pathogenic proteins predicted from short (100-150 bp) metagenomic reads and also performs on complete protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | pathogenic proteins, pathogenic proteins prediction, genomic data, metagenomic data, partial pathogenic proteins, partial pathogenic proteins prediction, complete protein sequences, bio.tools |
is listed by: bio.tools is listed by: Debian |
Institutional Research Fund of IISER Bhopal | PMID:24736651 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mp3 | https://bio.tools/mp3 | SCR_019282 | MP3 | 2026-08-14 09:28:28 | 2 | |||||
|
Bs-Seeker2 Resource Report Resource Website 1+ mentions |
Bs-Seeker2 (RRID:SCR_020948) | data processing software, software application, data analysis software, software resource, sequence analysis software | Software tool as versatile aligning pipeline for bisulfite sequencing data. Used for mapping bisulfite sequencing data and generating DNA methylomes. Improves mappability over existing aligners by using local alignment. Maps reads from RRBS library by building special indexes with improved efficiency and accuracy. Provides additional function for filtering out reads with incomplete bisulfite conversion, which is useful in minimizing overestimation of DNA methylation levels. | Versatile aligning pipeline, bisulfite sequencing data, mapping bisulfite sequencing data, generating DNA methylomes, DNA methylation level, reads mapping, Reduced Represented Bisulfite Sequencing library, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: BS Seeker has parent organization: University of California at Los Angeles; California; USA |
Institute of Genomics and Proteomics at UCLA ; NBRPC 2012CB316503; China Scholarship Council |
PMID:24206606 | Free, Available for download, Freely available | biotools:bs-seeker2 | http://pellegrini.mcdb.ucla.edu/BS_Seeker2/, https://bio.tools/bs-seeker2 | SCR_020948 | Bisulfite Sequencing Seeker2, BS Seeker2 | 2026-08-14 09:28:09 | 2 | |||||
|
MITE-Hunter Resource Report Resource Website 1+ mentions |
MITE-Hunter (RRID:SCR_020946) | data processing software, software application, data analysis software, software resource, sequence analysis software | Software pipeline to identify MITEs as well as other small Class 2 non autonomous Transposable Elements from genomic DNA data sets. Used for discovering miniature inverted repeat transposable elements from genomic sequences. Can search large genomic data sets including whole genome sequences. | Class 2 non-autonomous transposable element, genes non-coding regions, genome evolution, coding sequence, genomic DNA data sets, | NSF 0607123 | PMID:20880995 | Free, Available for download, Freely available | https://github.com/jburnette/MITE-Hunter | SCR_020946 | Miniature Inverted repeat Transposable Elements Hunter | 2026-08-14 09:28:29 | 7 | |||||||
|
gbs2ploidy Resource Report Resource Website |
gbs2ploidy (RRID:SCR_019290) | software toolkit, data processing software, software application, data analysis software, software resource | Software R package as functions for inference of ploidy from Genotyping By Sequencing data, including function to infer allelic ratios and allelic proportions in Bayesian framework. | Genotyping-by-sequencing data, GBS data, ploidy inference, allelic ratios infer, allelic proportions, Bayesian framework, ploidy level detection | is listed by: CRAN | PMID:28150424 | Free, Available for download, Freely available | SCR_019290 | 2026-08-14 09:28:29 | 0 | |||||||||
|
BayesEpiModels Web App Resource Report Resource Website 1+ mentions |
BayesEpiModels Web App (RRID:SCR_019292) | production service resource, web application, software resource, service resource, analysis service resource | Web app to help assess both short- and long-term forecasts of COVID-19 across the United States at multiple levels. Done by implementing one time-series model (ARIMA), one compartmental models (basic SIR), and six classical growth models, which all yield satisfactory prediction results in the past and current pandemics at early stage. | COVID-19, SARS-CoV-2, stochastic growth model, stochastic SIR model, Bayesian inference, | Free, Freely available | SCR_019292 | 2026-08-14 09:28:08 | 1 | |||||||||||
|
xiNET Resource Report Resource Website 10+ mentions |
xiNET (RRID:SCR_021010) | data processing software, web service, data access protocol, software application, software resource, data visualization software | Open source web based visualization tool for exploring crosslinking mass spectrometry results. Displays residue resolution positional information including linkage sites and linked peptides, all types of crosslinking reaction product, ambiguous results and additional sequence information such as domains. | Crosslinking mass spectrometry data visualization, linkage sites, linked peptides, crosslinking reaction product display, crosslink network maps, maps with residue resolution | Wellcome Trust | PMID:25648531 | Free, Available for download, Freely available | http://github.com/colin-combe/crosslink-viewer | SCR_021010 | Crosslink Network Maps With Residue Resolution | 2026-08-14 09:28:30 | 20 | |||||||
|
Biofactoid Resource Report Resource Website 1+ mentions |
Biofactoid (RRID:SCR_021011) | knowledge environment resource, project portal, portal, web service, data or information resource, data access protocol, software resource | Web tool for creating digital profile of scientific discoveries in article and connecting them to related research. Authors describe molecular interactions supported by their results, letting researchers explore first hand account of article findings and connect to related articles and knowledge. Web based system for scientists to compose structured representation of networks of interactions between genes, their products, and chemical compounds, represented using power of formal ontology. | Knowledge management, molecular interactions, pathway, compose network structured representation, digital profile, connect related articles, formal ontology |
is related to: Biological Pathways Exchange is related to: Biological Pathways Exchange has parent organization: University of Toronto; Ontario; Canada has parent organization: Harvard University; Cambridge; United States has parent organization: University of Oregon; Oregon; USA |
NHGRI U41HG006623; DARPA Big Mechanism |
Free, Freely available | SCR_021011 | 2026-08-14 09:28:18 | 1 | |||||||||
|
ChiRA Resource Report Resource Website 1+ mentions |
ChiRA (RRID:SCR_019219) | software toolkit, data processing software, workflow, data or information resource, training material, software application, software resource, narrative resource | Software tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. | RNA-RNA interactome experimental data, experimental data analysis, miRNA, RNA-RNA interactome, RNA structurome, CLASH, CLEAR-CLIP, PARIS, SPLASH, chimeric read, read, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:chira | https://rna.usegalaxy.eu/, https://bio.tools/chira | SCR_019219 | Chimeric Read Analyzer | 2026-08-14 09:28:28 | 6 | |||||||
|
cgmapotools Resource Report Resource Website 1+ mentions |
cgmapotools (RRID:SCR_020950) | data processing software, software application, data analysis software, software resource | Software package for DNA methylation analysis. Used for context-wise, gene-wise, bin-wise, region-wise and sample-wise analysis and visualizations. Used to improve precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data. | DNA methylomes analysis, DNA methylomes, context-wise analysis, gene-wise analysis, bin-wise analysis, region-wise analysis, sample-wise analysis, bisulfite sequencing data, allele specific methylation detection | National Key Research and Development Program of China ; National Natural Science Foundation of China |
PMID:28968643 | Free, Available for download, Freely available | SCR_020950 | 2026-08-14 09:28:17 | 3 | |||||||||
|
xProhet Resource Report Resource Website |
xProhet (RRID:SCR_021005) | data processing software, software application, data analysis software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 15, 2021. Software tool for analysis of cross-linked peptides. | PMID:24356771 | THIS RESOURCE IS NO LONGER IN SERVICE | http://proteomics.ethz.ch/cgi-bin/xquest2_cgi/download.cgi | SCR_021005 | xQuest/xProhet | 2026-08-14 09:28:18 | 0 | |||||||||
|
immuneML Resource Report Resource Website 1+ mentions |
immuneML (RRID:SCR_021004) | production service resource, portal, data or information resource, service resource, analysis service resource | Open source Python platform for machine learning based analysis and classification of adaptive immune receptors and repertoires. Supported by ELIXIR Norway. | Immune receptor, machine learning, predicting immune status, predicting antigen specificity | DOI:10.1101/2021.03.08.433891 | Free, Available for download, Freely available | SCR_021007 | https://galaxy.immuneml.uio.no/, https://github.com/uio-bmi/immuneML | SCR_021004 | 2026-08-14 09:28:30 | 1 | ||||||||
|
Hugging Face Resource Report Resource Website 100+ mentions |
Hugging Face (RRID:SCR_020958) | organization portal, data or information resource, community building portal, portal | Portal to build, train and deploy state of the art models powered by reference open source in natural language processing. | Hugging Face, Inc., NLP, Natural Language Processing, build art models, deploy art models, reference open source | Free, Freely available | https://github.com/huggingface | SCR_020958 | 2026-08-14 09:28:10 | 121 |
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.
