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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
MetaCyto Resource Report Resource Website 1+ mentions |
MetaCyto (RRID:SCR_016415) | data analysis software, data processing software, software application, software resource, software toolkit | Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database. | automated, analysis, meta, flow, cytometry, data, bio.tools |
is listed by: Bioconductor is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: The Immunology Database and Analysis Portal (ImmPort) |
the National Institute of Allergy and Infectious Diseases HHSN272201200028C | Free, Available for download, Freely available | biotools:metacyto | https://bio.tools/metacyto | SCR_016415 | 2026-08-21 12:40:49 | 5 | |||||||
|
Xenopus Express Resource Report Resource Website 1+ mentions |
Xenopus Express (RRID:SCR_016373) | XEP | biomaterial supply resource, material resource, organism supplier | Supplier of Frogs and Tadpoles for the scientific community. | RIN, Resource Information Network, xenopus, frog, tadpole, amphibian, supply, organism, diet, animal food, RRID Community Authority | is listed by: Resource Information Network | SCR_016373 | Xenopus Xpress | 2026-08-21 12:41:04 | 4 | |||||||||
|
Monica monitor Resource Report Resource Website |
Monica monitor (RRID:SCR_016416) | data or information resource, portal, topical portal | A peel and stick in-room ambulatory fetal monitoring solution by Monica Healthcare Ltd. Measures fetal heart rate (FHR), maternal heart rate (MHR) and uterine activity (UA). | instrument, ambulatory, fetal, monitoring, heart, rate, fetal, maternal, uterine, activity | has parent organization: University of Nottingham; Nottingham; United Kingdom | Commercially available | SCR_016416 | 2026-08-21 12:41:04 | 0 | ||||||||||
|
CycIF.org Resource Report Resource Website 10+ mentions |
CycIF.org (RRID:SCR_016267) | CycIF.org | data or information resource, experimental protocol, immuno detection protocol, immunofluorescence, narrative resource, web page | Web page for cyclic immunofluorescence. It lists several downloadable data and software pertaining to cyclic immunofluorescence. | immunofluorescence, cyclic, cycif, data, software, single cell, numeric, dataset, intratumoural, heterogeneity | has parent organization: LINCS Data Portal | NHLBI U54 HL127365 | PMID:26399630 | Public | SCR_016267 | cycif.org | 2026-08-21 12:40:41 | 16 | ||||||
|
Center for Expanded Data Annotation and Retrieval Resource Report Resource Website 1+ mentions |
Center for Expanded Data Annotation and Retrieval (RRID:SCR_016269) | CEDAR | controlled vocabulary, data or information resource, ontology, organization portal, portal | Develops information technologies that make authoring complete metadata more manageable. Its products aim to facilitate using the metadata in further research.Center to improve metadata and its use throughout biomedical sciences. Develops information technologies that make authoring complete metadata more manageable through better interfaces, terminology, metadata practices, and analytics. Optimizes metadata pathway from provider to end user. Provides way for funders to specify what metadata they want to collect as part of research life cycle. | Metadata, interface, metadata practice, analytics, metadata pathway, funded research, data repository, data collection, |
is related to: Stanford University; Stanford; California is related to: Yale University; Connecticut; USA is related to: University of Oxford; Oxford; United Kingdom has parent organization: Stanford Center for Biomedical Informatics Research is parent organization of: CEDAR Workbench |
NIAID U54 AI117925 | SCR_018150 | https://more.metadatacenter.org/ | SCR_016269 | 2026-08-21 12:40:42 | 4 | |||||||
|
easyGV Resource Report Resource Website 1+ mentions |
easyGV (RRID:SCR_016260) | data analysis software, data processing software, software application, software resource | Software for calculating different measures of glycaemic variability (GV). It analyzes continuous glucose monitoring data using a simple interface. | glycaemic, glycemia, variability, gv, glucose, diabetes, excel |
has parent organization: University of Oxford; Oxford; United Kingdom is a plug in for: Microsoft Excel |
PMID:21714681 | Free for academic use, Free for non-commercial use, Available for download | SCR_016260 | 2026-08-21 12:40:41 | 5 | |||||||||
|
Illumina: MiSeqDx System Resource Report Resource Website 1+ mentions |
Illumina: MiSeqDx System (RRID:SCR_016380) | instrument resource | MiSeqDx System is FDA-regulated, CE-IVD-marked, NGS platform for in vitro diagnostic (IVD) testing. System offers both diagnostic and research modes. | Illumina, Sequencing System, Instrument Equipment, USEDit, | Restricted | SCR_020137, Model_Number_MiSeqDx | SCR_016380 | MiSeqDx | 2026-08-21 12:40:47 | 2 | |||||||||
|
Illumina: HiSeq X Resource Report Resource Website 50+ mentions |
Illumina: HiSeq X (RRID:SCR_016385) | instrument resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 15,2023. Sequencer for whole-genome sequencing. System consists of HiSeq X ultra-high-throughput instruments that deliver over 18,000 human genomes per year. | Illumina, Sequencing System, Instrument Equipment, USEDit, | THIS RESOURCE IS NO LONGER IN SERVICE | Model_Number_HiSeq X, SCR_020131 | https://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/datasheet-hiseq-x-ten.pdf | SCR_016385 | HiSeq X | 2026-08-21 12:40:47 | 62 | ||||||||
|
Illumina: HiSeq 2500 System Resource Report Resource Website 50+ mentions |
Illumina: HiSeq 2500 System (RRID:SCR_016383) | instrument resource | High-throughput sequencing system. High-quality data using proven Illumina SBS chemistry has made it the instrument of choice for major genome centers and research institutions throughout the world.HiSeq 2500 System has been discontinued. Illumina will support the instrument and intends to supply the reagents through February 28, 2023. | Illumina, Sequencing System, Instrument Equipment, USEDit, | works with: PySeq2500 | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_016383.pdf | SCR_020123, Model_Number_HiSeq 2500 | https://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/hiseq2500/hiseq-2500-system-guide-15035786-03.pdf, https://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/hiseq2500/hiseq-2500-system-guide-15035786-03.pdf | https://www.illumina.com/systems/sequencing-platforms/hiseq-2500.html | SCR_016383 | HiSeq 2500 | 2026-08-21 12:40:47 | 88 | ||||||
|
PhenoSpD Resource Report Resource Website 1+ mentions |
PhenoSpD (RRID:SCR_016359) | PSD | data analysis software, data processing software, software application, software resource, software toolkit | Software toolkit for phenotypic correlation estimation and multiple testing correction (Spectral Decomposition, SpD) for human phenome using genome-wide association study (GWAS) summary statistics. It is a command line R based tool. | spectral, decomposition, matrice, phenotypic, correlation, estimation, multiple, testing, correction, human, phenome, genome, summary, statistic, decomposition, matrice, genomics |
is related to: University of Bristol; Bristol; United Kingdom is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_016359 | Pheno Spectral Decomposition, PhenoSpD | 2026-08-21 12:40:45 | 6 | ||||||||
|
Deeptools Resource Report Resource Website 1000+ mentions |
Deeptools (RRID:SCR_016366) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Python based tools to process, visualize and analyse high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. Implemented within Galaxy framework. Used to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. | process, visualize, analysis, sequencing, data, ChIP-seq, RNA-seq, MNase-seq, quality, control, normalization, aligned, read, clustering, bioinformatic | works with: Galaxy | German Epigenome Programme DEEP 01KU1216G; German Research Foundation SFB 992 |
PMID:27079975 | Free, Available for download, Freely available | http://deeptools.ie-freiburg.mpg.de/ | SCR_016366 | 2026-08-21 12:40:46 | 2806 | |||||||
|
SMAGEXP Resource Report Resource Website 1+ mentions |
SMAGEXP (RRID:SCR_016360) | SMAGEXP | data analysis software, data processing software, software application, software resource, software toolkit | Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more. | transcriptomics, data, meta, analysis, MicroArrays, RNA-Seq, Galaxy, gene, expression, next, generation, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: Gene Expression Omnibus is related to: metaMA is related to: metaRNASeq |
PMID:30698691 | Free, Available for download, Freely available | biotools:SMAGEXP | https://bio.tools/SMAGEXP | SCR_016360 | Statistical Meta Analysis for Gene EXPression | 2026-08-21 12:40:45 | 2 | |||||
|
XLSTAT Resource Report Resource Website 100+ mentions |
XLSTAT (RRID:SCR_016299) | XLSTAT | data analysis software, data management software, data processing software, data visualization software, software application, software resource | Software for commercial data analysis and statistical software package for Microsoft Excel. | data, process, manage, analyze, visualize, graph, statistic, microsoft, excel | is related to: Microsoft Excel | Addinsoft | Commercially available, Trial available | SCR_016299 | XL STATistics | 2026-08-21 12:40:43 | 175 | |||||||
|
TraCeR Resource Report Resource Website 10+ mentions |
TraCeR (RRID:SCR_016338) | data analysis software, data processing software, simulation software, software application, software resource, software toolkit | Software application for recovery of T cell receptor (TCR) data from single cell data. Used to reconstruct full-length, paired T cell receptor (TCR) sequences from T lymphocyte single-cell RNA sequence data. Links T cell specificity with functional response by revealing clonal relationships between cells alongside their transcriptional profiles. | recovery, receptor, single, cell, data, computation, method, reconstruct, sequence, T lymphocyte, RNA, sequence |
is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is related to: European Bioinformatics Institute |
European Research Council ; the Lister Institute for Preventative Medicine (S.A.T.) |
PMID:26950746 | Free, Available for download, Freely available | SCR_016338 | 2026-08-21 12:40:53 | 14 | ||||||||
|
migec Resource Report Resource Website 10+ mentions |
migec (RRID:SCR_016337) | MIGEC | data analysis software, data processing software, software application, software resource, software toolkit | Software package for analysis of immune repertoire sequencing data. Used for recovery of T Cell Receptor ( TCR ) data from bulk population data.Used for high-throughput sequencing data analysis. Allows for error correction while preserving the natural diversity of complex immune repertoires. | high sequencing, molecular, identifier, guided, error, correction, data, analysis, immune, recovery, T cell receptor, | European Regional Development Fund ; Molecular and Cell Biology program RAS ; Russian Foundation for Basic Research ; Russian President |
PMID:24793455 | Free, Available for download, Freely available | SCR_016337 | Molecular Identifier Guided Error Correction | 2026-08-21 12:40:45 | 11 | |||||||
|
clustree Resource Report Resource Website 100+ mentions |
clustree (RRID:SCR_016293) | data analysis software, data processing software, data visualization software, software application, software resource | Software package which allows to produce clustering trees and visualize clusterings at different resolutions. Used in the analysis of large data sets to group together samples with similar properties. | clustering, tree, visualisation, data, set, group, sample, similar, property, different, resolution, cluster | is related to: R Project for Statistical Computing | Free, Freely available, Available for download | https://github.com/lazappi/clustree | SCR_016293 | 2026-08-21 12:40:43 | 100 | |||||||||
|
NExT-EMA Resource Report Resource Website |
NExT-EMA (RRID:SCR_016291) | data analysis software, data processing software, software application, software resource | Software for combined elementary flux mode and network-embedded thermodynamic analysis. | efm, net, thermodynamics, flux, elementary, ema, stoichiometry | PMID:29237121 | Free, Available for download | SCR_016291 | 2026-08-21 12:40:43 | 0 | ||||||||||
|
FluxModeCalculator Resource Report Resource Website 1+ mentions |
FluxModeCalculator (RRID:SCR_016290) | data analysis software, data processing software, software application, software resource | Software for performing flux mode analysis in stoichiometric models. FluxModeCalculator enables large-scale elementary flux mode (EFM) computation and uses the OpenMP API to optimally exploit processor architectures with multiple cores., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | efm, flux, stoichiometry, algorithm, matlab, linux, model, magnitude, bio.tools |
is listed by: Debian is listed by: bio.tools |
Biobanking and Biomolecular Resources Research Infrastructure (BBMRI) ; CardioVascular Research Netherlands (CVON-ENERGISE) ; Center of Medical Systems Biology (CMSB) ; European Network for Genetic and Genomic Epidemiology (ENGAGE) ; Netherlands Consortium for Systems Biology (NCSB) |
PMID:26685305 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fluxmodecalculator, OMICS_10894 | https://bio.tools/fluxmodecalculator | SCR_016290 | Flux Mode Calculator | 2026-08-21 12:41:03 | 1 | |||||
|
FLIR tools Resource Report Resource Website 10+ mentions |
FLIR tools (RRID:SCR_016330) | data analysis software, data processing software, image analysis software, software application, software resource | Software application for thermography for FLIR Systems. It has a basic thermal image analysis function including color palette and image adjustment function. Used to analyse the thermographic measurement data. | thermography, FLIR Systems, image, data, measurement, analysis | Free, Available for download | SCR_016330 | 2026-08-21 12:40:44 | 16 | |||||||||||
|
star-for-criu Resource Report Resource Website 1+ mentions |
star-for-criu (RRID:SCR_016294) | alignment software, data processing software, image analysis software, software application, software resource | Software as an Hot Start software container for STAR alignment using CRIU (Checkpoint Restore in Userspace) tool to freeze the running container. Can be deployed to align RNA sequencing data. Used in the processing of biomedical big data for better reproducibility and reliability. | hot, start, container, star, aligner, sequencing, data, processing, biomedical, cloud, reproducibility, RNA, analysis, computing, environment | is related to: Systems Transcriptional Activity Reconstruction | AMEDD Advanced Medical Technology Initiative ; NHLBI U54 HL127624; NIGMS R01 GM126019 |
Free, Freely available, Available for download | https://github.com/paizhang/Hotstarting-For-STAR-Alignment | SCR_016294 | 2026-08-21 12:40:43 | 1 |
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 dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET 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 dkNET then you can log in from here to get additional features in dkNET 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 dkNET 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.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
Email: info_at_ dknet.org
