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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
cwl-metrics Resource Report Resource Website 1+ mentions |
cwl-metrics (RRID:SCR_017076) | CWL-metrics | software resource, software toolkit, software library | Software framework to collect and analyze computational resource usage of workflow runs based on common workflow language CWL. Used to share set of tools packaged in containers. Enables users to choose proper cloud instance for workflow runs based on run time metrics data. Operating system Unix/Linux. | collect, analyze, computational, resource, usage, workflow, common, language, container, cloud, data, analysis | is listed by: OMICtools | Japan Science and Technology Agency | DOI:10.1101/456756 | Free, Available for download, Freely available | OMICS_32746 | SCR_017076 | Common Workflow Language-metrics, common workflow language metrix | 2026-02-16 09:49:09 | 1 | |||||
|
rnaSPAdes Resource Report Resource Website 50+ mentions |
rnaSPAdes (RRID:SCR_016992) | software application, data processing software, sequence analysis software, data analysis software, software resource | Software tool for assembling transcripts from RNA-Seq data. Explores surprising computational parallels between assembly of transcriptomes and single cell genomes. Suitable for all kind of organisms. Part of SPAdes package since version 3.9. | assembling, transcript, RNA-Seq, data, single, cell, genome, analysis, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: SPAdes is related to: rnaQUAST |
Russian Science Foundation 14-50-00069 | DOI:10.1101/420208 | Free, Available for download, Freely available | biotools:rnaSPAdes_autogenerated | https://bio.tools/rnaSPAdes_autogenerated | SCR_016992 | 2026-02-16 09:49:08 | 53 | ||||||
|
Mayo Clinic Rochehster Bioinformatics Core Facility Resource Report Resource Website 1+ mentions |
Mayo Clinic Rochehster Bioinformatics Core Facility (RRID:SCR_017161) | Mayo Clinic Bioinformatics Core | core facility, access service resource, data analysis service, analysis service resource, production service resource, service resource | Core assists in genomics, proteomics and metabolomics data acquisition, management, analyses and interpretation to Mayo investigators. Participates in Basic science research, Clinical trials, Population health, and Translational science to execute analytical workflows and manage large omics data sets. Provides support to Mayo Clinic Center for Individualized Medicine and Mayo Clinic Cancer Center. Has its academic home in Department of Health Sciences Research within Division of Biomedical Statistics and Informatics. | bioinformatics, data, acquisition, management, analysis, genomics, proteomics, metabolomics | has parent organization: Mayo Clinic | Restricted | SCR_017161 | Bioinformatics Core, Division of Biomedical Statistics and Informatics, Rochehster, Mayo Clinic, Core Facility | 2026-02-16 09:49:10 | 2 | ||||||||
|
Max Planck Institiute of Immunobiology and Epigenetics Bioinformatics Core Facility Resource Report Resource Website |
Max Planck Institiute of Immunobiology and Epigenetics Bioinformatics Core Facility (RRID:SCR_017160) | core facility, access service resource, data analysis service, analysis service resource, software resource, production service resource, service resource | Core provides assistance in primary analysis of sequencing data and other large scale biocomputing. For our internal users we host extensive web services, workflows and customized tools that help with data management, visualizations, standardized analyses and data sharing. | bioinformatics, biocomputing, sequencing, data, omics, analysis, visualization, management | has parent organization: Max Planck Institiute of Immunobiology and Epigenetics; Freiburg; Germany | Restricted | SCR_017160 | , Bioinformatics Facility, Core Facility, Bioinformatics Core Facility, Epigenetics, Max Planck Institiute of Immunobiology | 2026-02-16 09:49:10 | 0 | |||||||||
|
CytExpert Software Resource Report Resource Website 500+ mentions |
CytExpert Software (RRID:SCR_017217) | software application, data processing software, data analysis software, software resource, data acquisition software | Software program that controls instrument operation, data collection and analysis. Software for CytoFLEX Platform by Beckman Coulter. | control, instrument, data, collection, analysis, CytoFLEX Platform, Beckman Coulter, flow, cytometry |
is listed by: OMICtools works with: Beckman Coulter CytoFLEX LX Flow Cytometer |
OMICS_30185 | SCR_017217 | 2026-02-16 09:49:11 | 888 | ||||||||||
|
PennAI Resource Report Resource Website |
PennAI (RRID:SCR_017215) | software application, data processing software, data visualization software, data analysis software, data management software, software resource | Open source software tool to leverage supervised machine learning techniques to analyze data. Can assist with tasks such as choosing appropriate models for data. Data science assistant for generating results from large and complex data problems. | Supervised, machine, learning, technique, data, mining, storing, analysis, visualizationn, artificial, intelligence | has parent organization: University of Pennsylvania; Philadelphia; USA | Free, Available for download, Freely available | http://pennai.org/ https://epistasislab.github.io/pennai/ |
SCR_017215 | Accessible artificial intelligence from University of Pennsylvania | 2026-02-16 09:49:11 | 0 | ||||||||
|
University of Oxford Medical Sciences Division Computational Genomics: Analysis and Training Core Facility Resource Report Resource Website |
University of Oxford Medical Sciences Division Computational Genomics: Analysis and Training Core Facility (RRID:SCR_017173) | CGAT | training service resource, core facility, access service resource, data analysis service, analysis service resource, production service resource, service resource, data or information resource | Core provides genomics training, as well as assistance in next generation sequencing analyses. | bioinformatics, genomics, next, generation, sequencing, data, analysis | has parent organization: University of Oxford; Oxford; United Kingdom | Restricted | SCR_017173 | Medical Sciences Division, Computational Genomics: Analysis and Training Core Facility, CGAT, University of Oxford, Computational Genomics Analysis and Training Core Facility | 2026-02-16 09:49:10 | 0 | ||||||||
|
Montreal Clinical Research Bioinformatics Core Facility Resource Report Resource Website |
Montreal Clinical Research Bioinformatics Core Facility (RRID:SCR_017176) | IRCM BIF, BIF | training service resource, core facility, access service resource, data analysis service, analysis service resource, production service resource, service resource, data or information resource | Core to support scientists within and outside IRCM in analysis of biological and clinical data, in particular high throughput genomic data. Operating on collaborative basis and paid services. Provides assistance with Data analysis for RNA-Seq, ChIP-Seq, RIP-Seq, DNA methylation, DNA-Seq, targeted sequencing of rRNAs, microarrays, customized training courses. | bioinformatics, genomic, omics, data, analysis, RNA-Seq, CHIP-Seq, RIP-Seq, DNA, methylation, DNA-Seq, rRNA, microarray | Restricted | SCR_017176 | , Institute of Clinical Research of Montreal, IRCM, Bioinformatics Core Facility, BIF | 2026-02-16 09:49:11 | 0 | |||||||||
|
Centre for Genome Regulation Bioinformatics Core Facility Resource Report Resource Website |
Centre for Genome Regulation Bioinformatics Core Facility (RRID:SCR_017145) | Biocore CRG | training resource, core facility, access service resource, software resource, service resource | Provides services of consultation and data analysis, with focus on Next Generation Sequencing and other high throughput experiments, software and database development, and training in basic and advanced bioinformatics techniques. Services provided for fee to support collaborative grant funded investigations. | bioinformatics, NGS, consultation, data, analysis, next, generation, sequencing | has parent organization: Centre for Genomic Regulation; Barcelona; Spain | Restricted | SCR_017145 | Bioinformatics Core, , Core Facility, Centre for Genomic Regulation, Biocore, CRG | 2026-02-16 09:49:10 | 0 | ||||||||
|
Bruker WinEPR program Resource Report Resource Website 1+ mentions |
Bruker WinEPR program (RRID:SCR_017023) | software application, data processing software, data analysis software, software resource, data acquisition software | Software tool to operate the EMX series of spectrometers by Bruker. Provides rapid data analysis of 1D and 2D data sets, provides environment for acquisition and processing of CW-EPR and CW-ENDOR spectra with the EMXplus and EMXmicro series of spectrometers. | operate, EMX, serie, spectrophotometer, Bruker, data, analysis, 1D, 2D, dataset, acquisition, processing, CW-EPR, CW-ENDOR | Commercially available | SCR_017023 | 2026-02-16 09:49:08 | 1 | |||||||||||
|
OMTools Resource Report Resource Website 1+ mentions |
OMTools (RRID:SCR_017143) | software application, data processing software, software toolkit, data visualization software, data analysis software, image analysis software, software resource, alignment software | Software package for optical mapping data processing, analysis and visualization. Used to handle and explore large scale optical mapping profiles. | optical, mapping, data, processing, analysis, visualization, large, scale, profile, phylogenesis | is listed by: SoftCite | Food and Health Bureau of the Hong Kong Special Administrative Region ; Chinese University of Hong Kong ; HKSAR Research Grants Council ; Lo Kwee-Seong Biomedical Research Fund ; Lee Hysan Foundation |
PMID:28505226 | Free, Available for download, Freely available | SCR_017143 | 2026-02-16 09:49:10 | 2 | ||||||||
|
PCAGO Resource Report Resource Website 1+ mentions |
PCAGO (RRID:SCR_017033) | web service, data access protocol, analysis service resource, software resource, production service resource, service resource | Interactive web service for analysis of RNA-Seq read count data with principal component analysis (PCA) and agglomerative clustering. Includes features like read count normalization, filtering read counts by gene annotation and visualization options. | analysis, RNAseq, read, count, data, principal, component, analysis, PCA, agglomerative, clustering, normalization, filtering, gene, annotation, visualization | is listed by: OMICtools | Deutsche Forschungsgemeinschaft (DFG) ; International Leibniz Research School for Microbial and Biomolecular Interactions |
DOI:10.1101/433078 | Free, Freely available | OMICS_32232 | SCR_017033 | 2026-02-16 09:49:09 | 7 | |||||||
|
NeuroAnatomy Toolbox Resource Report Resource Website 1+ mentions |
NeuroAnatomy Toolbox (RRID:SCR_017248) | NAT | software application, data processing software, data visualization software, data analysis software, software resource, 3d visualization software | Software R package for 3D visualisation and analysis of biological image data, especially tracings of single neurons. | 3D, visualization, analysis, data, image, single, neuron, tracing |
is listed by: OMICtools is related to: R Project for Statistical Computing has parent organization: MRC Laboratory of Molecular Biology |
Restricted | OMICS_18884 | http://jefferislab.github.io. https://CRAN.R-project.org/package=nat |
SCR_017248 | nat, , NeuroAnatomy Toolbox | 2026-02-16 09:49:11 | 4 | ||||||
|
pKiss Resource Report Resource Website 1+ mentions |
pKiss (RRID:SCR_017256) | software application, data processing software, sequence analysis software, data analysis software, software resource | Software tool for folding RNA secondary structures, including two limited classes of pseudoknots. Performs abstract shape analysis for structures holding pseudoknots up to complexity of kissing hairpin motifs. Successor of pknotsRG. Used for secondary structure prediction including kissing hairpin motifs. | folding, RNA, secondary, structure, pseudoknot, abstract, shape, analysis, hairpin, motif | is listed by: OMICtools | PMID:25273103 | Free, Available for download, Freely available | SCR_017256 | pKISS | 2026-02-16 09:49:12 | 4 | ||||||||
|
Deep Blue Epigenomic Data Server Resource Report Resource Website 1+ mentions |
Deep Blue Epigenomic Data Server (RRID:SCR_017490) | web service, access service resource, data access protocol, software resource, service resource, data or information resource | Central data access hub for large collections of epigenomic data. It organizes data from different sources using controlled vocabularies and ontologies. Data Server for storing, organizing, searching, and retrieving genomic and epigenomic data, handling associated metadata, and to perform different types of analysis. | Data, epigenomic, collection, ontology, storing, distributing, organizing, retriving, searching, genetic, metadata, analysis |
uses: ENCODE uses: Blueprint Epigenome uses: NIH Roadmap is related to: Roadmap Epigenomics Project |
German Science Ministry ; EU |
Free, Freely available | SCR_017490 | 2026-02-16 09:49:15 | 2 | |||||||||
|
DIANA-mirPath Resource Report Resource Website 100+ mentions |
DIANA-mirPath (RRID:SCR_017354) | web service, data analysis service, analysis service resource, data access protocol, software resource, production service resource, service resource | Web tool for integrating human and mouse microRNAs in pathways.Pathway analysis web-server, providing statistics, while being able to accommodate advanced pipelines. Web server for assessment of miRNA regulatory roles and identification of controlled pathways. Supports all analyses for KEGG molecular pathways and Gene Ontology (GO) in seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Gallus gallus and Danio rerio).DIANA miRPath v.2.0 includes investigating combinatorial effect of microRNAs in pathways.DIANA-miRPath v3.0 includes deciphering microRNA function with experimental support., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Pathway, analysis, statistics, assessment, miRNA, identify, regulatory, role, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Thessaly; Thessaly; Greece is provided by: DIANA Tools works with: KEGG works with: Gene Ontology |
European Social Fund ; John S. Latsis Public Benefit Foundation ; Development Grants For Research Institutions – KRIPIS ; General Secretariat for Research and Technology ; Ministry of Education ; Greece ; European Regional Development Fund |
PMID:25977294 PMID:19435746 PMID:22649059 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017495, biotools:diana-mirpath | http://diana.imis.athena-innovation.gr/DianaTools/ http://www.microrna.gr/miRPathv3 https://bio.tools/diana-mirpath |
http://www.microrna.gr/miRPathv2 | SCR_017354 | miRPath, miRPathv3, miRPathv2, DIANA-miRPath v2.0, DIANA-miRPath v3.0 | 2026-02-16 09:49:13 | 366 | ||||
|
PathwayNet Resource Report Resource Website 1+ mentions |
PathwayNet (RRID:SCR_017353) | web service, data analysis service, analysis service resource, data access protocol, software resource, production service resource, service resource | Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks. | Interface, interaction, predict, human, gene, network, integrative, analysis, user, data, tissue, cell, functional, protein, genome |
is listed by: OMICtools has parent organization: Princeton University; New Jersey; USA |
NIGMS R01 GM071966; NHGRI HG005998; NIGMS P50 GM071508 |
PMID:25431329 | Free, Freely available | SCR_017353 | 2026-02-16 09:49:13 | 7 | ||||||||
|
microMS Resource Report Resource Website 1+ mentions |
microMS (RRID:SCR_017443) | software application, data processing software, image processing software, image analysis software, software resource | Software Python platform for image guided Mass Spectrometry profiling. Provides graphical user interface for automatic cell finding and point based registration from whole slide images. Simplifies single cell analysis with feature rich image processing. | Image, guided, mass, spectrometry, automatic, cell, finding, point, based, registration, whole, slide, image, analysis, processing, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA |
NIDA DA018310; NIMH U01 MH109062; National Science Foundation Graduate Research Fellowship Program ; Springborn Fellowship ; NIGMS T32 GM070421 |
PMID:28593377 | Free, Available for download, Freely available | SCR_017443 | microscopy guided Mass Spectrometry | 2026-02-16 09:49:14 | 1 | |||||||
|
Relacs Resource Report Resource Website 1+ mentions |
Relacs (RRID:SCR_017280) | software application, data processing software, data analysis software, software resource, data acquisition software | Software platform for closed loop data acquisition, online analysis, and stimulus generation specifically designed for, but not limited to, electrophysiological recordings. | data, acquisition, analysis, electrophysiology, neuronal, response, control, stimulation | Free, Available for download, Freely available | SCR_017280 | Control, and Stimulation, Relaxed Electrophysiological Data Acquisition | 2026-02-16 09:49:12 | 2 | ||||||||||
|
Vesselucida 360 Resource Report Resource Website 1+ mentions |
Vesselucida 360 (RRID:SCR_017320) | VL360 | software application, data processing software, data visualization software, data analysis software, image analysis software, software resource, 3d visualization software, segmentation software | Software tool for visualization and automatic reconstruction of microvascular networks in 3D environment with built-in analysis tools by MBF Bioscience. | MBF Bioscience, vasculature, reconstruction, image, analysis, 3D, vessel, data, automatic, quantify, anastomoses, microvascular |
is used by: SPARC Portal works with: Vesselucida Explorer |
Restrcited | https://learn.mbfbioscience.com/vle.html | SCR_017320 | Vesselucida 360, Vesselucida | 2026-02-16 09:49:12 | 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 NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF 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 NIF then you can log in from here to get additional features in NIF 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 NIF 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.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
