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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Rice_HxD_Recovery_Metabolomics Resource Report Resource Website 1+ mentions |
Rice_HxD_Recovery_Metabolomics (RRID:SCR_017204) | software application, data analysis software, source code, software resource, data processing software, data visualization software | Software tool as source code used in analysis of GC MS data from rice samples. Workflow for statistical analysis of GC MS data from field grown rice collected during rewatering after exposure to combined drought and heat stress. | analysis, GC-MS, data, rice, sample, statistics, workflow | Free, Available for download, Freely available | SCR_017204 | 2026-07-28 09:44:28 | 1 | |||||||||||
|
University of Cambridge Department of Plant Sciences Bioinformatics Core Facility Resource Report Resource Website |
University of Cambridge Department of Plant Sciences Bioinformatics Core Facility (RRID:SCR_017164) | University of Cambridge Bioinformatics Core Facility | service resource, data analysis service, production service resource, access service resource, analysis service resource, core facility | Core provides assistance in data analysis to support members of Plant Sciences. | bioinformatics, data, analysis, service | has parent organization: University of Cambridge; Cambridge; United Kingdom | SCR_017164 | Department of Plant Sciences, Core Facility, Bioinformatics, University of Cambridge | 2026-07-28 09:44:27 | 0 | |||||||||
|
UCSF Gladstone Institutes Bioinformatics Core Facility Resource Report Resource Website |
UCSF Gladstone Institutes Bioinformatics Core Facility (RRID:SCR_017178) | UCSF Gladstone Institutes Bioinformatics Core | service resource, data or information resource, data analysis service, software resource, production service resource, access service resource, analysis service resource, core facility, training service resource | Core provides consulting services, sequencing, data analysis, and programming assistance. Used for Experimental Design and Power Analysis Consultation, RNA-seq, ChIP-seq, ATAC-seq analysis, Statistics consulting, Variant calling, Data normalization across multiple projects, General programming, Custom Figures for publication, tutorials for learning common software tools. | Bioinformatics, consulting, data, analysis, sequencing, RNA-seq, DNA-seq, ChIP-seq, ATAC-seq, statistics, variant, calling, normalization | Open | SCR_017178 | Bioinformatics Core, Gladstone Core Services, University California San Fransisco, UCSF, Gladstone Institutes | 2026-07-28 09:44:30 | 0 | |||||||||
|
Bonsai Resource Report Resource Website 50+ mentions |
Bonsai (RRID:SCR_017218) | software application, software resource, data processing software, data acquisition software | Software event based framework for processing and controlling data streams. Visual language designed for making software systems that require rich and rapid interaction with external world. | Event, based, framework, processing, controlling, data, stream | European Union Seventh Framework Programme ; Bial Foundation ; Foundation for Science and Technology ; Champalimaud Foundation |
PMID:25904861 | Free, Available for download, Freely available | https://github.com/bonsai-rx/bonsai-rx.github.io | SCR_017218 | 2026-07-28 09:44:32 | 88 | ||||||||
|
University of Manchester Bioinformatics Core Facility Resource Report Resource Website 1+ mentions |
University of Manchester Bioinformatics Core Facility (RRID:SCR_017171) | Manchester Bioinformatics Facility | service resource, data analysis service, software resource, production service resource, access service resource, analysis service resource, core facility | Core provides assistance in integrative analysis of genomic datasets to support faculty. | bioinformatics, analysis, genomic, data, dataset | has parent organization: University of Manchester; Manchester; United Kingdom | Restricted | SCR_017171 | , Bioinformatics Facility, University of Manchester, Bioinformatics Core Facility | 2026-07-28 09:44:31 | 2 | ||||||||
|
PIVOT software Resource Report Resource Website 10+ mentions |
PIVOT software (RRID:SCR_017210) | PIVOT | software application, software resource, data analysis software, data processing software | Software R package for interactive analysis and visualization of transcriptomics data. Operating systems are macOS, Linux, Windows. | Interactive, analysis, visualization, transcriptomics, data | is related to: University of Pennsylvania; Philadelphia; USA | NIMH U01 MH098953 | PMID:29304726 | Free, Available for download, Freely available | SCR_017210 | Platform for Interactive analysis and Visualization Of Transcriptomics, PIVOT, KimLabIDV | 2026-07-28 09:44:31 | 17 | ||||||
|
Vall dHebron Institut de Recerca Statistics and Bioinformatics Unit Core Facility Resource Report Resource Website |
Vall dHebron Institut de Recerca Statistics and Bioinformatics Unit Core Facility (RRID:SCR_017175) | UEB | service resource, data or information resource, data analysis service, software resource, production service resource, access service resource, analysis service resource, core facility, training service resource | Core at Vall dHebron Institut de Recerca, Barcelona, Spain to provide data analysis, softwares and training programs in statistics and bioinformatics for clinical research at VHIR. | bioinformatics, next, generation, sequencing, data, analysis, DNA, RNA, omics, microarray, RTqPCR, metagenomics, methylation | Restricted | SCR_017175 | , Barcelona, Vall dHebron Institut de Recerca, Support Unit in Methodology for Biomedical Research, UEB, Statistics and Bioinformatics Unit, USMIB | 2026-07-28 09:44:30 | 0 | |||||||||
|
Duke University Omics Data Analysis Core Facility Resource Report Resource Website |
Duke University Omics Data Analysis Core Facility (RRID:SCR_017174) | service resource, data or information resource, data analysis service, production service resource, access service resource, analysis service resource, core facility, training service resource | Genomic Analysis and Bioinformatics core for data analysis associated with performing complex and data intensive projects in life science research of Duke University and Duke Medical School. Provides expertise, training, data analysis in next generation sequencing, array and proteomic based technologies. | bioinformatics, data, analysis, training, expertise, next, generation, sequencing, array, proteomic, omics | has parent organization: Duke University; North Carolina; USA | Restricted | SCR_017174 | Analysis Core, Resource, Core Facility, Genomic Analysis and Bioinformatics, Duke University, Omics Data | 2026-07-28 09:44:31 | 0 | |||||||||
|
Rikshospitalet-Radiumhospitalet and University of Oslo Bioinformatics Core Facility Resource Report Resource Website |
Rikshospitalet-Radiumhospitalet and University of Oslo Bioinformatics Core Facility (RRID:SCR_017152) | BCF | service resource, data or information resource, data analysis service, database, production service resource, access service resource, analysis service resource, core facility | Core facility provides high throughput sequencing data analysis, metagenomics data analysis, proteomics data analysis, protein structure analysis, functional genomics, programming, scripting, and database or web services. | metagenomics, proteomics, protein, structure, functional, genomics, programming, scripting, data | Restricted | SCR_017152 | BCF, Core Facility, University of Oslo, Rikshospitalet-Radiumhospitalet, Bioinformatics | 2026-07-28 09:44:27 | 0 | |||||||||
|
Mass spectrometry imaging workbench Resource Report Resource Website 50+ mentions |
Mass spectrometry imaging workbench (RRID:SCR_017410) | software application, software resource, data analysis software, data processing software | Software tool for analysis of mass spectrometry imaging data implemented in Galaxy framework. Provides options to analyze mass spectrometry imaging data in imzML file format, including quality control, visualization, preprocessing, statistical analysis, image co-registration and feature identification.Galaxy docker container for mass spectrometry imaging. | Analysis, mass, spectrometry, imaging, data, Galaxy, framework, imzML, file, quality, control, visualization, statistics, docker, container | is related to: University of Freiburg; Baden-Wurttemberg; Germany | DOI:10.1101/628719 | Free, Available for download, Freely available | https://github.com/foellmelanie/docker-galaxy-msi, https://galaxyproject.org/use/msi/ | SCR_017410 | 2026-07-28 09:44:35 | 98 | ||||||||
|
CentroidFold Resource Report Resource Website 10+ mentions |
CentroidFold (RRID:SCR_017253) | software application, data access protocol, software resource, web service, simulation software | Web server for RNA secondary structure prediction. Predicts RNA secondary structure from RNA sequence. Based on generalized centroid estimator. | RNA, secondary, structure, prediction, centroid, estimator, sequecne, data, alignment, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
New Energy and Industrial Technology Development Organization of Japan ; Ministry of Education ; Culture ; Sports ; Science and Technology of Japan ; Internal fund of Computational Biology Research Center |
PMID:19435882 | Free, Freely available | biotools:centroidfold, OMICS_03449 | https://bio.tools/centroidfold | SCR_017253 | 2026-07-28 09:44:28 | 15 | ||||||
|
CFX Manager Resource Report Resource Website 100+ mentions |
CFX Manager (RRID:SCR_017251) | software application, software resource, data analysis software, data processing software | Software tool to analyze real-time PCR data and run PCR system in software controlled mode., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | RT PCR, real time PCR, data, analysis, BioRad | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017251 | CFX Manager software | 2026-07-28 09:44:32 | 489 | |||||||||
|
3D de novo assembly Resource Report Resource Website 10+ mentions |
3D de novo assembly (RRID:SCR_017227) | software application, software resource, data analysis software, data processing software | Software tool as 3D de novo assembly (3D DNA) pipeline. Used to help generate HI-C assembly. | de novo, assembly, 3D, DNA, HI-C, data, scaffold, pipeline, chromosome, genome | DOI:10.1126/science.aal3327 | Free, Available for download, Freely available | SCR_017227 | 2026-07-28 09:44:28 | 40 | ||||||||||
|
Connectome Computation System Resource Report Resource Website 10+ mentions |
Connectome Computation System (RRID:SCR_017342) | CCS | software application, software resource, data analysis software, data processing software | Software tool for multimodal human brain imaging data analysis. Computational pipeline for discovery science of human brain connectomes at macroscale with multimodal magnetic resonance imaging technologies. | Multimodal, human, brain, imaging, data, analysis, connectome, magnetic, resonance | DOI:10.1007/s11434-014-0698-3 | Free, Available for download, Freely available | SCR_017342 | 2026-07-28 09:44:29 | 15 | |||||||||
|
miRpathDB Resource Report Resource Website 50+ mentions |
miRpathDB (RRID:SCR_017356) | data or information resource, database, data access protocol, software resource, web service | Collection of single miRNAs that regulate pathways, gene ontologies and other categories, hence complementing available miRNA target enrichment programs, tailored for miRNA sets. New dictionary on microRNAs and target pathways. Database to augment available target pathway web-servers by providing researches access to information which pathways are regulated by miRNA, which miRNAs target pathway and how specific regulations are. | Collection, miRNA, data, pathway, gene, ontology, dataset, dictionary, target, regulation, bio.tools |
is listed by: bio.tools is listed by: Debian |
Saarland University ; Germany |
PMID:27742822 | biotools:miRPathDb | https://bio.tools/miRPathDB | SCR_017356 | miRNA Pathway Dictionary Database | 2026-07-28 09:44:29 | 52 | ||||||
|
Computational Suite for Bioinformaticians and Biologists Resource Report Resource Website 1+ mentions |
Computational Suite for Bioinformaticians and Biologists (RRID:SCR_017234) | CSBB | software application, software resource, data analysis software, data processing software | Software package for analysis of sequencing data. Command line based bioinformatics suite to analyze biological data acquired through biological experiments. | analysis, sequencing, data, command, line, expression, normalization, convert | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_17554 | https://github.com/csbbcompbio | SCR_017234 | CSBB-v3.0, CSBB-v1.0, CSBB-v2.0, Computational Suite for Bioinformaticians and Biologists | 2026-07-28 09:44:32 | 6 | ||||||
|
fastMNN Resource Report Resource Website 1+ mentions |
fastMNN (RRID:SCR_017351) | software application, software resource, data analysis software, data processing software | Software tool to correct for batch effects in single-cell expression data using fast version of mutual nearest neighbors (MNN) method. | Correct, batch, effect, single, cell, expression, data, fast, version, mutual, nearest, neighbors | Free, Available for download, Freely available | SCR_017351 | Fast Mutual Nearest Neighbors | 2026-07-28 09:44:33 | 7 | ||||||||||
|
redbiom Resource Report Resource Website 1+ mentions |
redbiom (RRID:SCR_017285) | software application, service resource, data analysis software, data analysis service, data processing software, software resource, production service resource, analysis service resource | Software tool for allowing samples that contain microbiome features to be rapidly identified. Rapid sample discovery and feature characterization system. Integrated with existing analysis tools to enable fast, large scale microbiome searches and discovery of new microbiome relationships. Service for sample metadata and sample data. | microbiome, feature, identify, characterize, analysis, metadata, sample, data | PMID:31239397 | Free, Available for download, Freely available | SCR_017285 | 2026-07-28 09:44:32 | 5 | ||||||||||
|
SerialEM Resource Report Resource Website 100+ mentions |
SerialEM (RRID:SCR_017293) | software application, software resource, data processing software, data acquisition software | Software tool for automated EM data acquisition. Used for efficient tilt series acquisition and interface for image capture, display, and storage and for control of some aspects of microscope function. | automated, data, acquisition, tilt, image, capture, display, storage, microscope | NCRR RR00592; NIGMS P01 GM61306 |
PMID:16182563 | Restricted | SCR_017293 | 2026-07-28 09:44:32 | 213 | |||||||||
|
SynGO Resource Report Resource Website 100+ mentions |
SynGO (RRID:SCR_017330) | service resource, data or information resource, data analysis service, production service resource, ontology, controlled vocabulary, analysis service resource | Evidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms. | Synapse, evidence, curated, base, reference, analysis, omics, data, ontology, gene, annotation | uses: Gene Ontology | Stanley Center for Psychiatric Research at The Broad Institute of MIT and Harvard ; European Union ; CERCA Program/Generalitat de Catalunya ; NINDS NS36251; German Federal Ministry of Education and Research |
PMID:31171447 | Free, Freely available | SCR_017330 | Synaptic Gene Ontologies | 2026-07-28 09:44:33 | 134 |
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 nidm-terms Resources search. From here you can search through a compilation of resources used by nidm-terms and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that nidm-terms 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 nidm-terms then you can log in from here to get additional features in nidm-terms 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 nidm-terms 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.
