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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
CAIRN
 
Resource Report
Resource Website
CAIRN (RRID:SCR_019101) data visualization software, web service, data processing software, software application, data access protocol, software resource Web tool to graph all copy number alterations present in segment file. Custom data is permitted. Allows to display copy number alterations which overlap user specified region, to quantify number of amplified CNAs and deleted CNAs. Visualization tool to explore copy number alterations discovered in published cancer datasets. Intended to help oncology community observe of relative rates of amplification, deletion, and mutation of interesting genes and regions. Deleted CNAs quantification, Copy Number Alterations, segment file, data visualization, published cancer datasets CNAs, amplified CNA quantification Nine Girls Ask Foundation ;
NCI CA207729;
NIGMS GM132055;
NCI CA107263;
NCI CA177519;
NCI CA102310;
NIA AG033082;
NCI P30 CA138313
PMID:31923184 Free, Available for download, Freely available https://github.com/jrdelaney/CAIRN SCR_019101 Copy Alterations Intuitive Rendering Navigator 2026-02-13 10:58:24 0
iTools
 
Resource Report
Resource Website
10+ mentions
iTools (RRID:SCR_009626) iTools data repository, storage service resource, web service, software repository, data or information resource, service resource, data access protocol, software resource, database An infrastructure for managing of diverse computational biology resources - data, software tools and web-services. The iTools design, implementation and meta-data content reflect the broad NCBC needs and expertise (www.NCBCs.org). computational neuroscience, data, experiment control, hardware, imaging genomics, information specification, java, loni pipeline, model, ontology, os independent, metadata is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: National Centers for Biomedical Computing
has parent organization: Laboratory of Neuro Imaging
NIH Roadmap for Medical Research ;
NCRR U54-RR021813;
NIDA U54-DA021519;
NCI U54-CA121852;
NHGRI U54-HG004028;
NIGMS U54-GM072970;
NIBIB U54-EB005149;
NLM U54-LM008748
PMID:18509477 GNU Lesser General Public License nlx_155852 http://www.nitrc.org/projects/itools
http://www.loni.usc.edu/research/software
http://itools.loni.ucla.edu/ SCR_009626 ITools Resourceome, NCBC iTools 2026-02-13 10:56:28 45
HOMER
 
Resource Report
Resource Website
5000+ mentions
HOMER (RRID:SCR_010881) HOMER sequence analysis software, data processing software, data analysis software, software application, software resource Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++. motif, discovery, next, generation, sequencing, analysis, genomic, data is listed by: OMICtools
is related to: findMotif.pl
has parent organization: University of California at San Diego; California; USA
NURSA consortium grant ;
NIH HC088093;
NIDDK DK063491;
NCI CA52599;
NIGMS P50 GM081892;
Foundation Leducq Transatlantic Network Grant
PMID:20513432 OMICS_00483 http://biowhat.ucsd.edu/homer/index.html SCR_010881 HOMER, Hypergeometric Optimization of Motif EnRichment, Homer, Homer v4.5 2026-02-13 10:56:42 5370
SnapATAC
 
Resource Report
Resource Website
10+ mentions
SnapATAC (RRID:SCR_020981) data processing software, data analysis software, software toolkit, software application, software resource Software package for analyzing scATAC-seq datasets.Used to dissects cellular heterogeneity in unbiased manner and map trajectories of cellular states. Can process data from up to million cells. Incorporates existing tools into comprehensive package for analyzing single cell ATAC-seq dataset. scATAC-seq datasets analysis, dissects cellular heterogeneity, cellular states, map trajectories NCI K99 CA252020;
UCSD School of Medicine ;
NIMH U19 MH114831
PMID:33637727 Free, Available for download, Freely available https://github.com/r3fang/SnapATAC SCR_020981 Single Nucleus Analysis Pipeline for ATAC-seq 2026-02-13 10:58:26 22
Exemplar Microscopy Images of Tissues
 
Resource Report
Resource Website
1+ mentions
Exemplar Microscopy Images of Tissues (RRID:SCR_021052) EMIT immuno detection protocol, experimental protocol, data repository, storage service resource, 2d spatial image, image collection, data set, data or information resource, immunofluorescence, service resource, image, image repository, narrative resource Reference dataset of multiplexed immunofluorescence microscopy images collected at HMS Laboratory of Systems Pharmacology. Includes set of images of different types for development and benchmarking of computational methods for image processing. As of 4/2/2021, EMIT comprises tissue microarray containing cores from 34 cancer, non-neoplastic diseases, and normal tissue collected from clinical discards under IRB supervised protocol. TMA was imaged using cyclic immunofluorescence method. Additional extensions of EMIT are currently in the planning stages. Long term goal is to compose ImageNet like resource for highly multiplexed images of tissues and tumors by consolidating high quality curated datasets. Reference dataset, multiplexed immunofluorescence microscopy images, tissue microarray, cyclic immunofluorescence, tissues images, tumors images is related to: Synapse
is related to: Harvard Medical School; Massachusetts; USA
glioblastoma, lung adenocarcinoma, prostate adenocarcinoma, seminoma, meningioma, mesothelioma, GI stromal tumor, liver cirrhosis, leiomyosarcoma, high-grade serous ovarian cancer, diverticulitis, acute appendicitis, metastatic melanoma, dedifferentiated liposarcoma NIH U54 CA225088;
NCI U2C CA233262;
NCI U2C CA233280;
Ludwig Center at Harvard Medical School and the Ludwig Cancer Research Foundation
DOI:10.1101/2021.03.15.435473 Restricted SCR_021052 Exemplar Microscopy Images of Tissues ( and Tumors) 2026-02-13 10:58:27 3
CNVpytor
 
Resource Report
Resource Website
10+ mentions
CNVpytor (RRID:SCR_021627) sequence analysis software, data processing software, data analysis software, software application, software resource Software Python package and command line tool for CNV/CNA analysis from depth of coverage by mapped reads. Software tool for CNV/CNA detection and analysis from read depth and allele imbalance in whole genome sequencing. Copy number variations, copy number alternations, whole genome sequencing, Python has parent organization: Mayo Clinic NCI U24 CA220242 DOI:10.1101/2021.01.27.428472 Free, Available for download, Freely available SCR_021627 2026-02-13 10:58:36 19
VAMPIRE
 
Resource Report
Resource Website
1+ mentions
VAMPIRE (RRID:SCR_021721) data processing software, data analysis software, software application, software resource, image analysis software Software tool for analysis of cell and nuclear morphology from fluorescence or bright field images. Enables profiling and classification of cells into shape modes based on equidistant points along cell and nuclear contours. Robust method to quantify cell morphological heterogeneity. cell morphology analysis, nuclear morphology analysis, fluorescence images, bright field images NCI U54 CA143868;
NCI R01 CA174388;
NIA P30 AG021334;
NIA U01 AG060903
DOI:10.1038/s41596-020-00432-x Free, Available for download, Freely available SCR_021721 Visually Aided Morpho-Phenotyping Image Recognition 2026-02-13 10:58:34 2
Cumulus
 
Resource Report
Resource Website
1+ mentions
Cumulus (RRID:SCR_021644) data analysis software, software resource, data processing software, software application Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data. Single cell genomics, spatial transcriptomics, single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire, data uses: Pegasus
uses: Cirrocumulus
uses: Pegasus-fus
is listed by: Terra
is related to: BICCN
has parent organization: Broad Institute
Klarman Cell Observatory ;
Manton Foundation ;
HHMI ;
Ludwig Center at MIT ;
Leidos Biomedical Research ;
Frederick National Laboratory for Cancer Research ;
NCI
DOI:10.1038/s41592-020-0905-x Free, Available for download, Freely available https://app.terra.bio/#workspaces/kco-tech/Cumulus
https://github.com/klarman-cell-observatory/cumulus/blob/91336094646217564a4f8e7b31c03c3c6bf2e84b/docs/index.rst
SCR_021644 2026-02-13 10:58:34 2
Motif Mutation Analysis for Regulatory Genomic Elements
 
Resource Report
Resource Website
500+ mentions
Motif Mutation Analysis for Regulatory Genomic Elements (RRID:SCR_021902) MMARGE data processing software, data analysis software, software toolkit, software application, software resource Software package that integrates genome wide genetic variation with epigenetic data to identify collaborative transcription factor pairs. Optimized to work with chromatin accessibility assays such as ATAC-seq or DNase I hypersensitivity, as well as transcription factor binding data collected by ChIP-seq. Used to identify combinations of cell type specific transcription factors while simultaneously interpreting functional effects of non-coding genetic variation. genome wide genetic variation, epigenetic data, identify collaborative transcription factor pairs, interpreting functional effects, non-coding genetic variation NCI CA173903;
NIGMS GM085764;
NIDDK DK091183;
NHLBI R00 123485
PMID:29893919 Free, Available for download, Freely available SCR_021902 2026-02-13 10:58:40 608
tximport
 
Resource Report
Resource Website
50+ mentions
tximport (RRID:SCR_016752) data analysis software, software resource, data processing software, software application Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis. pseudoaligned, reads, R, differential, expression, analysis, gene, transcript, bio.tools is listed by: Bioconductor
is listed by: Debian
is listed by: bio.tools
works with: edgeR
works with: DESeq2
SNSF 143883;
European Commission ;
NCI T32 CA009337
DOI:10.12688/f1000research.7563.1 Free, Available for download, Freely available biotools:tximport https://bioconductor.org/packages/tximport/
https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html
https://github.com/F1000Research/tximport
https://bio.tools/tximport
https://zenodo.org/record/35123#.W_w3behKiM8 SCR_016752 tximport v1.4.0 2026-02-13 10:57:50 91
Polysolver
 
Resource Report
Resource Website
10+ mentions
Polysolver (RRID:SCR_022278) data analysis software, software resource, data processing software, software application Software tool for HLA typing based on whole exome sequencing data and infers alleles for three major MHC class I genes. Enables accurate inference of germline alleles of class I HLA-A, B and C genes and subsequent detection of mutations in these genes using inferred alleles as reference. HLA typing, whole exome sequencing data, accurate inference of germline alleles, high precision HLA-typing, alleles of class I HLA-A, B and C genes, detection of mutations, inferred alleles has parent organization: Broad Institute Blavatnik Family Foundation ;
NHLBI 1RO1HL103532;
NCI 1R01CA155010;
AACR
PMID:26372948 Free, Available for download, Freely available SCR_022278 POLYmorphic loci reSOLVER, POLYSOLVER 2026-02-13 10:58:40 30
CytoTRACE
 
Resource Report
Resource Website
100+ mentions
CytoTRACE (RRID:SCR_022828) software resource, simulation software, software application Software tool that predicts differentiation state of cells from single cell RNA sequencing data. Used for predicting differentiation states from scRNA-seq data. differentiation state of cells, single cell RNA sequencing data, predicting differentiation states, scRNA-seq data NCI R00CA187192;
NCI R01CA100225;
Stinehart Reed foundation ;
Stanford Bio-X Interdisciplinary Initiatives Seed Grants Program ;
Virginia and D.K. Ludwig Fund for Cancer Research ;
U.S. Department of Defense ;
National Science Foundation Graduate Research Fellowship ;
Stanford Bio-X Bowes Graduate Student Fellowship ;
Stanford Medical Science Training Program
PMID:31974247 Free, Freely available SCR_022828 Cellular (Cyto) Trajectory Reconstruction Analysis using gene Counts and Expression 2026-02-13 10:58:49 132
SvABA
 
Resource Report
Resource Website
10+ mentions
SvABA (RRID:SCR_022998) sequence analysis software, data processing software, data analysis software, software application, software resource Software tool for detecting structural variants in sequencing data using genome wide local assembly. Genome wide detection of structural variants and indels by local assembly. Used for detecting SVs from short read sequencing data using genome wide local assembly with low memory and computing requirements. genome wide detection, structural variants, indels, local assembly NHGRI T32 HG002295;
NCI U54CA143798;
NCI R01CA188228;
DFCI-Novartis Drug Discovery Program ;
Voices Against Brain Cancer ;
Pediatric Low-Grade Astrocytoma Foundation ;
Broad Institute ;
Wellcome Fund Career Award for Medical Scientists
PMID:29535149 Free, Available for download, Freely available SCR_022998 2026-02-13 10:58:58 14
Adenoma Polyp Tissue Bank
 
Resource Report
Resource Website
Adenoma Polyp Tissue Bank (RRID:SCR_005366) APTB biomaterial supply resource, material resource THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The Adenoma Polyp Tissue Bank (APTB) receives whole blood from patients enrolled in the Prevention of Sporadic Colorectal Adenomas with Celecoxib clinical trial. We have reached our accrual on blood submissions, so we will no longer be receiving blood specimens The objectives of this trial are as follows: A. To determine the efficacy and safety of celecoxib versus placebo in preventing the occurrence of newly detected colorectal adenomas in subjects at increased risk for colorectal carcinoma. In addition to incidence, other established risk factors will be evaluated for their association with occurrence of new colorectal adenomas, including cancer family history and adenoma size, histopathologic grade, multiplicity and location. Primary assessment of treatment efficacy will be the reduction in the number of subjects with adenomas at colonoscopy after Year 1 and Year 3 of study drug use. Secondary assessments of treatment efficacy will be 1) the number of adenomas 2) the histopathologic grade of adenomas and 3) the size of adenomas, also measured after one year and three years of study drug use. These factors will be incorporated into a risk model for predicting adenoma occurrence and response to celecoxib. B. To determine the efficacy of celecoxib versus placebo in modulating one or more of a panel of biomarkers for colorectal cancer at the cellular and molecular level sampled in a subset of subjects at selective sites at baseline and after Year 1 and Year 3 of study drug use. These biomarkers will include measurements of aberrant crypt foci (ACF), proliferation (index and crypt distribution), apoptosis (index and crypt distribution), COX expression and activity. If modulation of one or more mucosal biomarkers occur, we will explore whether it correlates with the development of incident colorectal neoplasia (adenomas/carcinomas), thereby attempting to validate the surrogacy of that biomarker. C. To develop a specimen bank. Serum and white blood cells are isolated from whole blood and adenoma tissue blocks and slides are banked. Banked specimens will become available for use in correlative science studies at a later point. This project began in 1999 and will be extended through 2006. The lead principal investigator is Monica M. Bertagnolli, MD, Brigham and Women''s Hospital, Boston, MA, and the APTB Director is Scott Jewell, Ph.D., Department of Pathology, The Ohio State University. The APTB is supported by the NIH, NCI Division of Cancer Prevention, in connection with the Strang Cancer Prevention Center, Cornell University, New York., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. blood, serum, white blood cell, adenoma tissue, tissue, whole blood, block, slide, colorectal adenoma, celecoxib, adenoma, cancer, colorectal cancer, clinical trial, polyp, risk factor is listed by: One Mind Biospecimen Bank Listing
has parent organization: Human Tissue Resource Network
has parent organization: Human Tissue Resource Network
Increased risk for colorectal carcinoma NCI THIS RESOURCE IS NO LONGER IN SERVICE nlx_144435 SCR_005366 APTB Specimen Bank 2026-02-13 10:55:37 0
North Carolina University at Chapel Hill School of Medicine High Throughput Peptide Synthesis and Array Core Facility
 
Resource Report
Resource Website
1+ mentions
North Carolina University at Chapel Hill School of Medicine High Throughput Peptide Synthesis and Array Core Facility (RRID:SCR_017837) core facility, access service resource, service resource Core offers services for: High quality synthetic peptides, stable isotope labeled peptides, peptides with PTM and fluorescent and affinity tags, synthesis of peptide libraries. Analysis of synthetic peptides. Purification, lyophilization and aliquoting of synthetic peptides. Synthetic, peptide, stable, isotope, labeled, library, analysis, purification, lyophilization, aliquoting, service, core, ABRF is listed by: ABRF CoreMarketplace NCI P30 CA016086 Open ABRF_626 SCR_017837 UNC High-Throughput Peptide Synthesis and Array Facility 2026-02-13 10:58:05 6
North Carolina University at Chapel Hill School of Medicine Macromolecular X-Ray Crystallography Core Facility
 
Resource Report
Resource Website
North Carolina University at Chapel Hill School of Medicine Macromolecular X-Ray Crystallography Core Facility (RRID:SCR_017839) MX Facility core facility, access service resource, service resource Core provides support and infrastructure necessary to initiate and successfully complete structural biology or structural chemistry project. Offers services in Crystallization,X-Ray DiffractionData Collection,Structure Determination and Refinement. Structural, biology, chemistry, X-ray, crystallography, diffraction, data, collection, refinement, service, core, ABRF is listed by: ABRF CoreMarketplace NCI P30 CA016086 Open ABRF_629 SCR_017839 Macromolecular X-Ray Crystallography 2026-02-13 10:58:03 0
New York University School of Medicine Langone Cytometry and Cell Sorting Core Facility
 
Resource Report
Resource Website
New York University School of Medicine Langone Cytometry and Cell Sorting Core Facility (RRID:SCR_018827) core facility, access service resource, service resource Facility provides cytometry and cell sorting services. Services include immunophenotyping, cell cycle analysis, and intracellular fluorophore detection. Services can be tailored to research needs, certified cytometrists are available to help plan experiments. Offers online and hands-on training in use of cell analyzers and analysis software. USEDit, flow cytometry service, cell sorting service, immunophenotyping, cell cycle analysis, intracellular fluorophore detection, , ABRF, ABRF is listed by: ABRF CoreMarketplace
is related to: USEDit
has parent organization: New York University; New York; USA
NCI P30 CA016087 Open ABRF_762 https://coremarketplace.org/?FacilityID=762 SCR_018827 New York University Cytometry and Cell Sorting Laboratory, Cytometry and Cell Sorting Laboratory 2026-02-13 10:58:18 0
Northwestern University Developmental Therapeutics Core Facility
 
Resource Report
Resource Website
1+ mentions
Northwestern University Developmental Therapeutics Core Facility (RRID:SCR_017948) DTC core facility, access service resource, service resource Core evaluates therapeutic agents and diagnostics, as well as existing therapeutics being considered for novel uses, through continued development and deployment of relevant animal models and in vitro cell lines and tissue models. Provides services to investigators to suit many needs, including those who may lack laboratory facilities and/or expertise for conducting experiments associated with preclinical therapeutic hypothesis testing.Services include Proliferation and Apoptosis Assays, Therapy-Response Experiments, Exploratory PK and Tox, Device Implantation and Monitoring,PDX Models,Immunization. Evaluate, therapeutic, agent, diagnostic, novel, animal, model, development, in vitro, cell, line, tissue, testing, proliferation, apoptosis, assay, therapy, response, immunization, service, core, ABRF is listed by: ABRF CoreMarketplace
has parent organization: Northwestern University; Illinois; USA
NCI CA060553 Open ABRF_947 https://coremarketplace.org/?FacilityID=947&citation=1 https://cdt.northwestern.edu/core-services/ SCR_017948 Developmental Therapeutics Core 2026-02-13 10:58:05 3
Northwestern University Proteomics Core Facility
 
Resource Report
Resource Website
1+ mentions
Northwestern University Proteomics Core Facility (RRID:SCR_017945) core facility, access service resource, service resource Core offers multiple types of experiments from simple protein identification to protein quantitation. Performs traditional bottom-up proteomics, where proteins are digested with enzyme prior to analysis and intact, top-down proteomics analyses. Services include proteins identification after in-gel or in-solution digestion, top-down mass spectrometry to preserve post-translationally modified forms of proteins present in vivo by measuring them intact, IP-MS Pulldown,BioID service to identify target of biotin ligase that has been tagged onto their protein via traditional cloning methods,Untargeted Quantitative Peptide Proteomics,Targeted Quantitative Peptide Proteomics,Epiproteomic Histone Modification Panel A,Epiproteomic Histone Modification Panel B,Untargeted Metabolomics,Phosphoproteomics,PTM Scan,ChIP-MS. Protein, indentification, quantitation, proteomics, analysis, enzyme, digestion, mass, spectrometry, peptide, targeted, epiproteomic, histone, modification, untargeted, phosphoproteomics, PTM Scan, ChIP-MS, service, core, ABRF is listed by: ABRF CoreMarketplace
is related to: USEDit
has parent organization: Northwestern University; Illinois; USA
NCI P30 CA060553;
NIH Office of the Director S10 OD025194;
NIGMS P41 GM108569
Open SCR_017880, ABRF_944 https://coremarketplace.org/?FacilityID=944 https://coremarketplace.org/?FacilityID=738 SCR_017945 Northwestern Proteomics, Northwestern University Proteomics Center of Excellence Core Facility 2026-02-13 10:58:05 5
University of Wisconsin-Madison Advanced Genome Editing Laboratory
 
Resource Report
Resource Website
1+ mentions
University of Wisconsin-Madison Advanced Genome Editing Laboratory (RRID:SCR_021070) AGEL core facility, access service resource, service resource Provides services and expertise to unlock genome editing tools to advance your research. Routinely generates new genome edited models, particularly mouse, rats, swine, and cell lines, as well as supports in vivo editing, novel preclinical therapeutic strategies, pooled lentiCRISPR screening, and other applications. USEDit, generating genome edited models, mouse, rats, swine, ABRF, ABRF, CRISPR, gene editing, genome editing, lentiCRISPR is listed by: ABRF CoreMarketplace
has parent organization: University of Wisconsin-Madison; Wisconsin; USA
NCI P30 CA014520 ABRF_1148 https://coremarketplace.org/?FacilityID=1148 SCR_021070 University of Wisconsin Madison UW-Genome Editing & Animal Models, UW-Genome Editing & Animal Models, University of Wisconsin Madison Advanced Genome Editing Laboratory, UW Biotechnology Center Advanced Genome Editing Laboratory, Genome Editing and Animal Models Core, University of Wisconsin Madison Genome Editing Core Facility, Transgenic Animal Facility 2026-02-13 10:58:27 9

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