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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.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Vancouver Prostate Centre Laboratory for Advanced Genome Analysis
 
Resource Report
Resource Website
1+ mentions
Vancouver Prostate Centre Laboratory for Advanced Genome Analysis (RRID:SCR_012394) VPC LAGA, LAGA access service resource, core facility, service resource Core offers sequencing and microarray services, solutions for the profiling of FFPE tissues, and complete, project-tailored downstream bioinformatics analysis. The core's structure enables the management of research projects from experimental design to analysis and interpretation of data as well as support for grant applications and publications. The LAGA provides open fee-for-service access as a core facility (intra-institutional services to its researchers) and as regional, national and international facility (inter-institutional services). Microarray, Profiling of FFPE, Analysis is listed by: ScienceExchange
is related to: Vancouver Prostate Centre Labs and Facilities
has parent organization: University of British Columbia; British Columbia; Canada
Available to external user SciEx_13 https://www.prostatecentre.com/our-research/core-facilities/LAGA https://www.scienceexchange.com/labs/laboratory-for-advanced-genome-analysis SCR_012394 , Laboratory for Advanced Genome Analysis, PC-TRiADD, VPC 2026-02-15 09:20:29 1
CHARMM
 
Resource Report
Resource Website
500+ mentions
CHARMM (RRID:SCR_014892) software application, simulation software, software resource Software program that simulates molecular interactions. It has features that allow broad application to many-particle systems with a comprehensive set of energy functions, a variety of enhanced sampling methods, and support for multi-scale techniques, and a range of implicit solvent models. It also primarily targets biological systems including peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments. CHARMM can also be applied to inorganic materials with applications in materials design and has a comprehensive set of analysis and model builiding tools. visualization, modeling, molecular simulation, materials design, model building tools, analysis, biological systems, peptides, proteins is used by: CHARMM-GUI SCR_014892 2026-02-15 09:21:04 936
Sanford Burnham Prebys Medical Discovery Institute Stem Cell Core
 
Resource Report
Resource Website
Sanford Burnham Prebys Medical Discovery Institute Stem Cell Core (RRID:SCR_014856) material resource, biomaterial supply resource THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The former functions of this facility are split into two separate operations. The first is the generation and characterization of induced Pluripotent Stem Cells (iPSCs) is now being performed on a collaborative basis for both internal and external investigators with the Snyder lab. The second is a shared laboratory dedicated to the culture and analysis of stem cells that is available to SBP investigators. stem cell, facility, la jolla, pluripotent stem cells, ipsc, analysis THIS RESOURCE IS NO LONGER IN SERVICE SCR_014856 SBP Medical Discovery Institute Stem Cell Core, SBP Stem Cell Core 2026-02-15 09:21:02 0
FLIMfit
 
Resource Report
Resource Website
1+ mentions
FLIMfit (RRID:SCR_016298) software application, software toolkit, software resource Software package for quantitative analysis of large Fluorescence Lifetime Imaging Microscopy (FLIM) data, including global analysis. It is able to routinely analyse multi-well plate FLIM datasets on conventional PC workstations in a reasonable time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. fluorescence, lifetime, imaging, microscopy, dataset, global, analysis, multiwell, plate, routine United Kingdom Biotechnology and Biological Sciences Research Council BBSRC BB/E003621/1;
United Kingdom Technology Strategy Board Technology Award CHBT/007/00030;
Wellcome Trust WT 095931/Z/11/Z
PMID:23940626
DOI:10.1371/journal.pone.0070687
THIS RESOURCE IS NO LONGER IN SERVICE https://github.com/flimfit/FLIMfit SCR_016298 2026-02-15 09:21:04 3
sleipner
 
Resource Report
Resource Website
1+ mentions
sleipner (RRID:SCR_018143) software toolkit, software resource Software package as collection of modules implementing methods of analysis that form self-contained and empirically grounded toolbox for handling longitudinal data within person oriented paradigm. Longitudinal data, analysis, cross sectional data, pattern oriented analysis, has parent organization: Stockholm University; Stockholm; Sweden Restricted SCR_018143 SLEIPNER, Sleipner, SLEIPNER 2.1 2026-02-15 09:22:10 2
meta
 
Resource Report
Resource Website
50+ mentions
meta (RRID:SCR_019055) software toolkit, software resource Software general R package providing standard methods for meta analysis. Meta analysis, standard methods, meta in R, analysis, statistics is listed by: CRAN
is related to: dmetar
has parent organization: University of Freiburg; Baden-Wurttemberg; Germany
DOI:10.1007/978-3-319-21416-0 Free, Available for download, Freely available https://cran.r-project.org/web/packages/meta/meta.pdf SCR_019055 meta in R 2026-02-15 09:21:47 61
CellChat
 
Resource Report
Resource Website
500+ mentions
CellChat (RRID:SCR_021946) software toolkit, software resource Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets. inference, visualization, analysis, cell-cell communication, single cell data, intercellular communication networks, single-cell RNA-sequencing data NSF DMS1763272;
Simons Foundation ;
NIH U01 AR073159;
NIGMS R01 GM123731;
NIH P30 AR07504;
Pew Charitable Trust ;
LEO Foundation ;
UC Irvine ;
Howard Hughes Medical Institute
PMID:33597522 Free, Available for download, Freely available http://www.cellchat.org/ SCR_021946 2026-02-15 09:22:11 536
Fusion ICA Toolbox
 
Resource Report
Resource Website
10+ mentions
Fusion ICA Toolbox (RRID:SCR_003494) FIT software application, data processing software, software toolkit, software resource A MATLAB toolbox which implements the joint Independent Component Analysis (ICA), parallel ICA and CCA with joint ICA methods. It is used to to extract the shared information across modalities like fMRI, EEG, sMRI and SNP data. * Environment: Win32 (MS Windows), Gnome, KDE * Operating System: MacOS, Windows, Linux * Programming Language: MATLAB * Supported Data Format: ANALYZE, NIfTI-1 analysis, functional magnetic resonance imaging, cca, image, eeg, neuroimaging, matlab, smri, snp, mri, algorithm, reusable library, independent component analysis, principal component analysis is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Biositemaps
has parent organization: University of New Mexico; New Mexico; USA
NIBIB 1RO1EB005846;
NSF 0612076
GNU General Public License nif-0000-36743 http://www.nitrc.org/projects/fit SCR_003494 Fusion ICA Toolbox (FIT) 2026-02-15 09:18:31 13
Gephi
 
Resource Report
Resource Website
1000+ mentions
Gephi (RRID:SCR_004293) Gephi software application, data processing software, software resource Open-source software for network visualization and analysis helping data analysts to intuitively reveal patterns and trends, highlight outliers and tells stories with their data. It uses a 3D render engine to display large graphs in real-time and to speed up the exploration. Gephi combines built-in functionalities and flexible architecture to: explore, analyze, spatialize, filter, cluterize, manipulate and export all types of networks. Gephi runs on Windows, Linux and Mac OS X. Gephi is based on a visualize-and-manipulate paradigm which allow any user to discover networks and data properties. Moreover, it is designed to follow the chain of a case study, from data file to nice printable maps. It is open-source and free (GNU General Public License). Applications: * Exploratory Data Analysis: intuition-oriented analysis by networks manipulations in real time. * Link Analysis: revealing the underlying structures of associations between objects, in particular in scale-free networks. * Social Network Analysis: easy creation of social data connectors to map community organizations and small-world networks. * Biological Network analysis: representing patterns of biological data. * Poster creation: scientific work promotion with hi-quality printable maps. Gephi 0.7 architecture is modular and therefore allows developers to add and extend functionalities with ease. New features like Metrics, Layout, Filters, Data sources and more can be easily packaged in plugins and shared. The built-in Plugins Center automatically gets the list of plugins available from the Gephi Plugin portal and takes care of all software updates. Download, comment, and rate plugins provided by community members and third-party companies, or post your own contributions! network, visualization, visual analytics, exploratory data analysis, graph, analysis, open source, plugin, filter, cluter, manipulate, export is parent organization of: Diseasome GNU General Public License nlx_31183 SCR_004293 2026-02-15 09:18:40 3059
FIVA - Functional Information Viewer and Analyzer
 
Resource Report
Resource Website
1+ mentions
FIVA - Functional Information Viewer and Analyzer (RRID:SCR_005776) FIVA software application, data processing software, software resource Functional Information Viewer and Analyzer (FIVA) aids researchers in the prokaryotic community to quickly identify relevant biological processes following transcriptome analysis. Our software is able to assist in functional profiling of large sets of genes and generates a comprehensive overview of affected biological processes. Currently, seven different modules containing functional information have been implemented: (i) gene regulatory interactions, (ii) cluster of orthologous groups (COG) of proteins, (iii) gene ontologies (GO), (iv) metabolic pathways (v) Swiss Prot keywords, (vi) InterPro domains - and (vii) generic functional categories. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible gene, gene expression, gene expression pattern, functional profile, statistical analysis, metabolic pathway, gene ontology, function, ortholog, gene regulatory interaction, biological process, transcriptome, visualization, analysis is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: MolGen
Netherlands Organization for Scientific Research ;
industrial partners in the NWO-BMI project number 050.50.206 on Computational Genomics of Prokaryotes ;
Center IOP Genomics ;
European Union QLK3-CT-2001-01473
PMID:17237043 Free for academic use nlx_149245 SCR_005776 FIVA - Functional Information Viewer Analyzer, Functional Information Viewer and Analyzer (FIVA), Functional Information Viewer and Analyzer 2026-02-15 09:19:03 1
GoBean - a Java application for Gene Ontology enrichment analysis
 
Resource Report
Resource Website
10+ mentions
GoBean - a Java application for Gene Ontology enrichment analysis (RRID:SCR_005808) GoBean software application, data processing software, software resource GoBean is a Java application for gene ontology enrichment analysis. It utilizes the NetBeans platform framework. Features * Graphical comparison of multiple enrichment analysis results * Versatile filter facility for focused analysis of enrichment results * Effective exploitation of the graphical/hierarchical structure of GO * Evidence code based association filtering * Supports local data files such as the ontology obo file and gene association files * Supports late enrichment methods and multiple testing corrections * Built-in ID conversion for common species using Ensembl biomart service Platform: Windows compatible, Mac OS X compatible, Linux compatible java, gene ontology, ontology, gene association, analysis, enrichment, term enrichment is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: Gachon University of Medicine and Science; Incheon; South Korea
PMID:22360891 Free for academic use nlx_149296 http://neon.gachon.ac.kr/GoBean/ SCR_005808 2026-02-15 09:19:12 22
SeqExpress
 
Resource Report
Resource Website
SeqExpress (RRID:SCR_007075) software application, data processing software, software resource A comprehensive analysis and visualization software package for gene expression experiments that provides: a number of clustering and analysis techniques; integrated gene expression and analysis result visualizations, integration with the Gene Expression Omnibus; and an optional data sharing architecture. GO is used to assign functional enrichment scores to clusters, using a combination of specially developed techniques and general statistical methods. These results can be explored using the in built ontology browsing tool or through the generated web pages. SeqExpress also supports numerous data transformation, projection, visualization, file export/import, searching, integration (with R), and clustering options. gene, gene expression, function, analysis, visualization, statistical analysis, windows, c#, gene function, chromosome location, bio.tools is listed by: Gene Ontology Tools
is listed by: bio.tools
is listed by: Debian
is related to: Gene Ontology
is related to: Gene Expression Omnibus
PMID:14988116 Free nlx_149285, biotools:seqexpress https://bio.tools/seqexpress SCR_007075 2026-02-15 09:19:21 0
BRAIN Initiative
 
Resource Report
Resource Website
10+ mentions
BRAIN Initiative (RRID:SCR_006770) NIH BRAIN Initiative organization portal, data or information resource, portal Project aimed at revolutionizing understanding of human brain, to show how individual cells and complex neural circuits interact, enable rapid progress in development of new technologies and data analysis tools to treat and prevent brain disorders. BRAIN Initiative encourages collaborations between neurobiologists and scientists from disciplines such as statistics, physics, mathematics, engineering, and computer and information sciences. Institutes and centers contributing to NIH BRAIN Initiative support those research efforts. brain, connectomics, disorder, cell, neural, circuit, neurotechnology, data, repository, analysis uses: Single Cell Portal
recommends: Human Neocortical Neurosolver
recommends: Brain Gene Expression Analysis toolbox
recommends: clusterExperiment
recommends: BioWheel
recommends: iELVis
recommends: Mediation Analysis of Causality under Confounding
recommends: MCell
recommends: microMS
recommends: MIIVsem
recommends: MountainSort
recommends: Myriads
recommends: nelpy
recommends: NetPyNE
recommends: Neural Ideal
recommends: NEURON
recommends: Neuron Tools
recommends: Neuroscience Gateway
recommends: NUTMEG
recommends: PetaVision
recommends: PyNWB
recommends: pyRayleighCuda
recommends: ScanImage
recommends: Scope
recommends: Seizure-Waves
recommends: Silver Lab Microscopy Software
recommends: StimVision
recommends: TReNA
recommends: ALICE
recommends: BioImage Suite
recommends: EyeWire
recommends: GIMME
recommends: GMA
recommends: Homer2
recommends: Brain Image Library
recommends: Data Archive BRAIN Initiative
recommends: OpenNeuro
recommends: Brain Observatory Storage Service and Database (BossDB)
recommends: 1000 Functional Connectomes Project
recommends: FastProject
recommends: Autopatcher
recommends: cytoNet
recommends: DiffuserCam
recommends: gene Expression Analysis Resource
recommends: NeMOarchive
recommends: Distributed Archives for Neurophysiology Data Integration
recommends: NIDA Data Share
recommends: HED Tags
lists: University of North Carolina Neuroscience Center and the BRAIN Initiative Viral Vector Core Facility
is related to: Brain Image Library
is related to: OpenNeuro
is related to: Distributed Archives for Neurophysiology Data Integration
is related to: NeMO Analytics
is related to: Brainome portal
is related to: CEMBA MethylC Seq Pipeline
is related to: Seattle Alzheimer Disease Brain Cell Atlas
is related to: EBRAINS
has parent organization: National Institutes of Health
is parent organization of: Data Archive BRAIN Initiative
is parent organization of: OpenNeuro
is parent organization of: Brain Observatory Storage Service and Database (BossDB)
is parent organization of: Ecosystem for Multi-modal Brain-behavior Experimentation and Research
has organization facet: 3D Developmental Mouse Brain Common Coordinate Framework
Alzheimer's disease, Schizophrenia, Autism, Epilepsy, Traumatic brain injury BRAIN Initiative nlx_155554 http://braininitiative.nih.gov/
http://www.whitehouse.gov/share/brain-initiative
http://en.wikipedia.org/wiki/BRAIN_Initiative
SCR_006770 , Brain Research through Advancing Innovative Neurotechnologies Initiative, NIH Brain Research through Advancing Innovative Neurotechnologies Initiative 2026-02-15 09:19:21 18
DSI Studio
 
Resource Report
Resource Website
500+ mentions
DSI Studio (RRID:SCR_009557) DSI Studio software application, image analysis software, data processing software, software resource A software for diffusion MR images analysis. The provided functions include reconstruction (DTI, QBI, DSI, and GQI), deterministic fiber tracking, and 3D visualization. It has a window-based interface and operates on Microsoft Windows system. analyze, c++, console (text based), dicom, diffusion mr fiber tracking, diffusion spectrum, fiber tracking, image reconstruction, linux, microsoft, modeling, magnetic resonance, nifti, posix/unix-like, q-ball, quantification, super tensor, tensor metric, tractography, visualization, win32 (ms windows), windows, coregistration, analysis is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Carnegie Mellon University; Pennsylvania; USA
BSD License nlx_155737 http://www.nitrc.org/projects/dsistudio SCR_009557 2026-02-15 09:20:04 558
Homer2
 
Resource Report
Resource Website
100+ mentions
Homer2 (RRID:SCR_009586) software application, image analysis software, data processing software, software resource Software matlab scripts used for analyzing fNIRS data to obtain estimates and maps of brain activation. Graphical user interface (GUI) for visualization and analysis of functional near-infrared spectroscopy (fNIRS) data. Analysis, optical, imaging, fnirs, map, brain, activation, BRAIN Initiative is recommended by: BRAIN Initiative
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: NIRx2nirs: A NIRx to .nirs data converter
NIBIB EB025145;
NIBIB R01 EB006385;
NCRR P41 RR14075
Free, Available for download, Freely available nlx_155773 http://www.nitrc.org/projects/homer2
https://homer-fnirs.org/
SCR_009586 HOMER1, Photon Migration Imaging toolbox 2026-02-15 09:19:46 223
DPABI
 
Resource Report
Resource Website
1000+ mentions
DPABI (RRID:SCR_010501) DPABI software application, data processing software, software toolkit, software resource Software toolbox for data processing and analysis of brain imaging, evolved from DPARSF (Data Processing Assistant for Resting-State fMRI). neuroimaging, resting-state fmri, brain, analysis, fmri uses: DPARSF
has parent organization: RFMRI.ORG
GNU General Public License nlx_158469 SCR_010501 DPABI: a toolbox for Data Processing & Analysis of Brain Imaging, toolbox for Data Processing and Analysis of Brain Imaging 2026-02-15 09:19:59 1048
Hunt Biobank
 
Resource Report
Resource Website
10+ mentions
Hunt Biobank (RRID:SCR_010626) HUNT Biobank material resource, cell repository, biomaterial supply resource International biobank storing whole blood and DNA from 200,000 individuals, serum and plasma samples from more than 100,000 individuals as well as urine, RNA tubes, cells, buffy coat and Na-heparin tubes for environmental analysis for as many as 50,000 individuals. All bio-specimens from the HUNT surveys are collected, processed and stored at the HUNT Biobank in Levanger. The National CONOR Biobank is located on the same site, where it serves as a central research repository for DNA samples from all the largest Norwegian health surveys. These make up the Cohorts of Norway (CONOR), which include samples from more than 200,000 individuals. * HUNT 1 was carried out in 1984-1986 to establish the health history of 75,000 people. * HUNT 2, carried out in 1995-1997, focused on the evolution of the health history of 74,000 people. This included blood sample collection from 65,000 people. The data that accompany biospecimens in the biobank are stored in secured computer systems that run complex database management and analysis software. * HUNT 3 was completed in June 2008. 93,210 people were invited to participate in the study, and as of the 6th of June, 2008, 48,289 people participated (52% participation rate). The data, collected by means of questionnaires, interviews, clinical examinations and collection of blood and urine samples, will be ready for analysis in January 2009. * Young-HUNT is the adolescent part of HUNT including participants aged 13-19 years. Young-HUNT1 (1995-97) was conducted as part of HUNT2, 9141 adolescents participated (90% response rate). Young-HUNT2 (2000-01) was a follow-up study of Young-HUNT1, 2400 students participated in both studies (77% of the invited). Young-HUNT3 (2006-08) was a new cross-sectional study as part of HUNT3. This time 8677 adolescents participated (87% response rate). Data collection included self-reported questionnaires, structured interviews, clinical measurements and, in Young-HUNT3, buccal smears. All institutions with research expertise can apply for access to analyze HUNT data. Projects must have recommendations from The Regional Committee for Medical Research in Norway (REK) and be registered with The Norwegian Social Science Data Services (NSD). longitudinal study, population, health, environment, whole blood, dna, serum, plasma, urine, rna, cell, buffy coat, na-heparin, blood, medical history, family medical history, adolescent, self-reported questionnaire, structured interview, clinical measurement, buccal smear, analysis, adult, adolescent, aging, FASEB list is listed by: One Mind Biospecimen Bank Listing
has parent organization: Norwegian University of Science and Technology; Trondheim; Norway
nlx_57833 http://www.huntbiosciences.com/default.asp?Valgt=Ja&Mode=Meny&MenyID=41&HovedMenyID=41&Hovedmeny=HUNT+Biobank SCR_010626 Nord-Tr��������ndelag health study Biobank, Nord-Trondelag health study, HUNT Databank 2026-02-15 09:20:23 48
qMRLab
 
Resource Report
Resource Website
qMRLab (RRID:SCR_016256) software application, image analysis software, data processing software, software resource Software for quantitative MR image analysis, simulation, and protocol optimization. It aims to provide the community with a tool for data fitting, plotting, simulation and protocol optimization for a variety of different quantitative models. mr, image, analysis, simulation, optimize, protocol Quebec Bio‐Imaging Network QBIN 8436‐0501;
Fonds de Recherche du Québec ‐ Nature et Technologies FRQNT 2015‐PR‐182754;
Natural Sciences and Engineering Research Council of Canada (NSERC) ;
Canadian Institute of Health Research (CIHR)
Open source, Free, Available for download SCR_016256 qMTLab, qMR Lab 2026-02-15 09:21:03 0
HMS LINCS Center
 
Resource Report
Resource Website
10+ mentions
HMS LINCS Center (RRID:SCR_016370) HMS LINCS organization portal, data or information resource, portal Center that is part of the NIH Library of Integrated Network-based Cellular Signatures (LINCS) Program. Its goals are to collect and disseminate data and analytical tools needed to understand how human cells respond to perturbation by drugs, the environment, and mutation. LINCS, Program, library, network, cell, signature, analysis, drugs, human, research is related to: HMS LINCS Database
has parent organization: Harvard Medical School; Massachusetts; USA
NHLBI U54 HL127365 PMID:29199020 SCR_016370 LINCS Center, Harvard Medical School LINCS Center, Harvard Medical School LINCS, Harvard Medical School (HMS) LINCS Center 2026-02-15 09:21:05 15
University of Pittsburgh Single Cell Core Facility
 
Resource Report
Resource Website
1+ mentions
University of Pittsburgh Single Cell Core Facility (RRID:SCR_025110) access service resource, core facility, service resource Core offers single cell sequencing. Provides analysis of transcriptomics, proteomics and epigenomics at single cell level. Provides comprehensive approach for cell characterization and gene expression profiling. Services include single cell gene expression, immune profiling, ATAC, and multiome analysis. ABRF, single cell sequencing, analysis, transcriptomics, proteomics, epigenomics is listed by: ABRF CoreMarketplace
has parent organization: University of Pittsburgh; Pennsylvania; USA
ABRF_2669 https://coremarketplace.org/?FacilityID=2669&citation=1 SCR_025110 University of Pittsburgh Single Cell Core 2026-02-15 09:23:44 5

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