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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
POAS4SPM
 
Resource Report
Resource Website
1+ mentions
POAS4SPM (RRID:SCR_010469) POAS4SPM software resource Software toolbox for SPM to denoise diffusion MRI data. Used for diffusion weighted magnetic resonance imaging data enhancement based on structural adaptive smoothing in both voxel space and diffusion-gradient space.Part of the ACID-toolbox. denoise diffusion MRI data, diffusion weighted, magnetic resonance imaging data, MRI data, is related to: ACID
works with: SPM
Deutsche Forschungsgemeinschaft ;
Wellcome Trust
PMID:24993814 nlx_157718 http://www.diffusiontools.com/ SCR_010469 Position Orientation Adaptive Smoothing for SPM 2026-09-12 12:57:19 9
T1DBase
 
Resource Report
Resource Website
100+ mentions
T1DBase (RRID:SCR_007959) data or information resource, data repository, database, resource, service resource, storage service resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 26,2019. In October 2016, T1DBase has merged with its sister site ImmunoBase (https://immunobase.org). Documented on March 2020, ImmunoBase ownership has been transferred to Open Targets (https://www.opentargets.org). Results for all studies can be explored using Open Targets Genetics (https://genetics.opentargets.org). Database focused on genetics and genomics of type 1 diabetes susceptibility providing a curated and integrated set of datasets and tools, across multiple species, to support and promote research in this area. The current data scope includes annotated genomic sequences for suspected T1D susceptibility regions; genetic data; microarray data; and global datasets, generally from the literature, that are useful for genetics and systems biology studies. The site also includes software tools for analyzing the data. genetics, beta cell, gene, variant, region, genomics, gene expression, genome-wide association study, data analysis service, bio.tools is used by: NIF Data Federation
is used by: NIDDK Information Network (dkNET)
is listed by: NIDDK Information Network (dkNET)
is listed by: Debian
is listed by: bio.tools
is related to: dkCOIN
has parent organization: University of Cambridge; Cambridge; United Kingdom
Type 1 diabetes. Diabetes Wellcome Trust ;
NIDDK ;
Juvenile Diabetes Research Foundation
PMID:20937630 THIS RESOURCE IS NO LONGER IN SERVICE. nif-0000-03531, biotools:t1dbase https://bio.tools/t1dbase SCR_007959 T1DBase - Type 1 Diabetes Database 2026-09-12 12:56:58 147
Rfam
 
Resource Report
Resource Website
1000+ mentions
Rfam (RRID:SCR_007891) Rfam, RFAM analysis service resource, data analysis service, data or information resource, database, production service resource, service resource The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: Non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion. Rfam is also available via FTP. You can find data in Rfam in various ways... * Analyze your RNA sequence for Rfam matches * View Rfam family annotation and alignments * View Rfam clan details * Query Rfam by keywords * Fetch families or sequences by NCBI taxonomy * Enter any type of accession or ID to jump to the page for a Rfam family, sequence or genome family, genome, clan, structure, non-coding rna, FASEB list has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom Howard Hughes Medical Institute ;
University of Manchester; Manchester; United Kingdom ;
Wellcome Trust WT077044/Z/05/Z
PMID:21062808 http://rfam.sanger.ac.uk/ SCR_007891 RFAM, Rfam database 2026-09-12 12:56:57 4040
BoxPlotR
 
Resource Report
Resource Website
100+ mentions
BoxPlotR (RRID:SCR_015629) data processing software, data visualization software, software application, software resource, web application Web tool written in R for generation of box plots with R packages shiny, beanplot4, vioplot, beeswarm and RColorBrewer, and hosted on shiny server to allow for interactive data analysis. Data are held temporarily and discarded as soon as session terminates.Represents both summary statistics and distribution of primary data. Enables visualization of minimum, lower quartile, median, upper quartile and maximum of any data set.Data matrix can be uploaded as file or pasted into application. May be downloaded to run locally or as virtual machine for VMware and VirtualBox. Box plot generation, customized box plot, data, plot, analysis is listed by: SoftCite
is related to: PlotsOfData
is related to: vioplot
ERC ;
Genome Québec International Recruitment Award ;
Wellcome Trust ;
WTCCB
PMID:24481215 Free, Available for download, Freely available SCR_018327 https://github.com/VizWizard/BoxPlotR.shiny SCR_015629 2026-09-12 12:58:28 370
Bio-tradis
 
Resource Report
Resource Website
50+ mentions
Bio-tradis (RRID:SCR_015993) TraDIS:Transposon Directed Insertion Sequencing data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. software, tool, analysis, data, sequencing, insertion, transponson, direct, mutant, library, perl, bio.tools is listed by: Debian
is listed by: bio.tools
is listed by: OMICtools
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
Alexander von Humboldt Stiftung/Foundation ;
Medical Research Council G1100100/1;
Wellcome Trust WT098051
PMID:26794317
DOI:10.1093/bioinformatics/btw022
Free, Available for download, Freely available OMICS_11083, biotools:bio-tradis https://bio.tools/bio-tradis, https://sources.debian.org/src/bio-tradis/ SCR_015993 2026-09-12 12:58:33 56
ChEMBL
 
Resource Report
Resource Website
1000+ mentions
ChEMBL (RRID:SCR_014042) data or information resource, database Collection of bioactive drug-like small molecules that contains 2D structures, calculated properties and abstracted bioactivities. Used for drug discovery and chemical biology research. Clinical progress of new compounds is continuously integrated into the database. database, compound, data, bioassay, bioactive, molecule, drug, discovery is used by: GEROprotectors
is used by: PubChem
is recommended by: NIDDK Information Network (dkNET)
is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
EMBL Member States ;
EU Innovative Medicines Initiative ;
GSK ;
Medicines for Malaria Ventures ;
Pfizer ;
Syngenta ;
Wellcome Trust
PMID:21948594 Public, Free, Freely available, Acknowledgement requested r3d100010539 https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320 SCR_014042 ChEMBLdb, Chembl, ChEMBL Database 2026-09-12 12:58:11 3035
SC3
 
Resource Report
Resource Website
10+ mentions
SC3 (RRID:SCR_015953) data analysis software, data processing software, sequence analysis software, software application, software resource Software tool for the unsupervised clustering of cells from single cell RNA-Seq experiments. SC3 is capable of identifying subclones from the transcriptomes of neoplastic cells collected from patients. scRNA-seq, interactive, cluster, clustering, cell, single, rna, rnaseq, bio.tools is listed by: Debian
is listed by: bio.tools
ARC (Action de Recherche Concerte) ;
Belgian Network DYSCO ;
Belgian State Science Policy Office ;
Bloodwise 13003;
Cambridge Experimental Cancer Medicine Centre ;
Cambridge NIHR Biomedical Research Center ;
EPSRC EP/N014529/1;
FRS-FNRS ;
Kay Kendall Leukaemia Fund ;
Leukemia and Lymphoma Society of America 07037;
MRC ;
Sanger Institute ;
University of Edinburgh ;
Wallonia-Brussels Federation ;
Wellcome Trust 104710/Z/14/Z
PMID:28346451 Free, Available for download biotools:sc3 https://bio.tools/sc3 SCR_015953 SC3 package, Single-Cell Consensus Clustering 2026-09-12 12:58:32 23
Stimfit
 
Resource Report
Resource Website
10+ mentions
Stimfit (RRID:SCR_016050) data analysis software, data processing software, software application, software resource Software for viewing and analyzing electrophysiological data. It features an embedded Python shell that allows you to extend the program functionality by using numerical libraries such as NumPy and SciPy. electrophysiology, python, numpy, scipy, numerical, library, stimulus, analysis uses: NumPy
uses: SciPy
European Research Council ;
Gatsby Charitable Foundation ;
Wellcome Trust
PMID:24600389 Free, Available for download SCR_016050 2026-09-12 12:58:34 41
Clonalframe
 
Resource Report
Resource Website
100+ mentions
Clonalframe (RRID:SCR_016060) data analysis software, data processing software, sequence analysis software, software application, software resource Software package for the inference of bacterial microevolution using multilocus sequence data. It is used to identify the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance. analysis, sequence, inference, bacteria, microevolution, multilocus, clonal, sample, chromosome, homologuous, recombination, disrupted, inheritance, DNA, genome is listed by: Debian
is listed by: OMICtools
is related to: Imperial College London; London; United Kingdom
is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
Wellcome Trust DOI:10.1534/genetics.106.063305 Free, Available for download OMICS_14623 https://github.com/xavierdidelot/ClonalFrameML, https://sources.debian.org/src/clonalframe/ SCR_016060 ClonalFrameML 2026-09-12 12:58:34 407
Gubbins
 
Resource Report
Resource Website
500+ mentions
Gubbins (RRID:SCR_016131) data analysis software, data processing software, sequence analysis software, software application, software resource Software application as an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. It is used for phylogenetic analysis of genome sequences and generating highly accurate reconstructions under realistic models of short-term bacterial evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. rapid, phylogenetic, analysis, large, sample, recombinant, bacteria, whole, genome, sequence, loci, elevated, densities, base, substitiution, mutatiion, outside, region, evolution, alignment is listed by: Debian
is listed by: OMICtools
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
Wellcome Trust 098051 PMID:25414349 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_14386 https://sources.debian.org/src/gubbins/ SCR_016131 Gubbins: Genealogies Unbiased By recomBinations In Nucleotide Sequences 2026-09-12 12:58:35 604
Brain Imaging Data Structure (BIDs)
 
Resource Report
Resource Website
100+ mentions
Brain Imaging Data Structure (BIDs) (RRID:SCR_016124) BIDS data or information resource, narrative resource, portal, standard specification Standard specification for organizing and describing outputs of neuroimaging experiments. Used to organize and describe neuroimaging and behavioral data by neuroscientific community as standard to organize and share data. BIDS prescribes file naming conventions and folder structure to store data in set of already existing file formats. Provides standardized templates to store associated metadata in form of Javascript Object Notation (JSON) and tab-separated value (TSV) files. Facilitates data sharing, metadata querying, and enables automatic data analysis pipelines. System to curate, aggregate, and annotate neuroimaging databases. Intended for magnetic resonance imaging data, magnetoencephalography data, electroencephalography data, and intracranial encephalography data. Data storing structure, neuroimaging, standardized template, data sharing, MRI data, MEG data, EEG data, iEEG data, FASEB list is used by: OpenNeuro
is used by: SPARC Portal
is used by: SPARC Data Standard
is listed by: FAIRsharing
is related to: BIDS-Matlab
is related to: NiPoppy
works with: MNE-BIDS
European Regional Development Fund ;
German federal state of Sachsen-Anhalt ;
International Neuroinformatics Coordinating Facility ;
Laura and John Arnold Foundation ;
Medical Research Council United Kingdom ;
NIAAA U01 AA021697;
NIGMS P20 GM103472;
NIMH Intramural Research Program ;
NSF 1429999;
Wellcome Trust
PMID:27326542
PMID:29917016
PMID:31239435
PMID:31239438
PMID:37744469
Free, Freely available https://bids-specification.readthedocs.io/en/stable/, https://doi.org/10.25504/FAIRsharing.rd1j6t SCR_016124 Brain Imaging Data Structure, BIDS, Brain Imaging Data Structure (BIDS), Brain Imaging Data Structure v1.4.0 2026-09-12 12:58:35 235
Jpred
 
Resource Report
Resource Website
100+ mentions
Jpred (RRID:SCR_016504) data analysis software, data analytics software, data processing software, sequence analysis software, software application, software resource Software tool for protein secondary structure prediction from the amino acid sequence by the JNet algorithm. Makes also predictions on Solvent Accessibility and Coiled-coil regions. protein, secondary, structure, prediction, amino, acid, sequence, accurate, JNet algorithm, solvent, accessibility, coiled, coil, region Biotechnology and Biological Sciences Research Council ;
Wellcome Trust 106370Z14;
Wellcome Trust 355804783;
Wellcome Trust WT083481;
Wellcome Trust WT092340
DOI:10.1093/nar/gkn238 Free, Available for download, Freely available,Tutorial available SCR_016504 Jprotein secondary structure PREDiction 2026-09-12 12:58:40 133
riboWaltz
 
Resource Report
Resource Website
10+ mentions
riboWaltz (RRID:SCR_016948) data analysis software, data processing software, data visualization software, software application, software resource Software R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Works for read alignments based on transcript coordinates. calculation, optimal, Psite, offset, diagnostic, analysis, visual, inspection, ribosome, profiling, data, read, alignment, transcript, coordinate uses: ggplot2
uses: Biostrings
uses: GenomicFeatures
uses: GenomicRanges
uses: IRanges
uses: devtools
is related to: R Project for Statistical Computing
Autonomous Province of Trento ;
Wellcome Trust
PMID:30102689 Free, Available for download, Freely available SCR_016948 2026-09-12 12:58:46 23
EnteroBase
 
Resource Report
Resource Website
100+ mentions
EnteroBase (RRID:SCR_019019) data access protocol, data or information resource, database, software resource, web service Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella. Bacteria, pathogen, genome, Illumina short read, genotype, core genome multilocus, sequence typing, cgMLST, cgMLST sequence, bacterial strain mapping, visualizing genomic variation, bio.tools, FASEB list is listed by: Debian
is listed by: bio.tools
has parent organization: University of Warwick; Coventry; United Kingdom
Biotechnology and Biological Sciences Research Council ;
Wellcome Trust
Restricted biotools:Enterobase https://bio.tools/EnteroBase SCR_019019 2026-09-12 12:59:08 317
SpydrPick
 
Resource Report
Resource Website
1+ mentions
SpydrPick (RRID:SCR_018176) data analysis software, data processing software, software application, software resource Software command line tool for performing direct coupling analysis of aligned categorical datasets. Used for analysis at scale of pan genomes of many bacteria. Incorporates correction for population structure, which adjusts for phylogenetic signal in data without requiring explicit phylogenetic tree. Direct coupling analysis, aligned categorical datasets, analysis, genome, bacteria, phylogenetic signal, correction, phylogenetic tree, data, bio.tools is listed by: Debian
is listed by: bio.tools
COIN Center of Excellence ;
Academy of Finland ;
European Research Council ;
Wellcome Trust
PMID:31361894 Free, Available for download, Freely available biotools:SpydrPick https://anaconda.org/bioconda/spydrpick, https://bio.tools/SpydrPick SCR_018176 2026-09-12 12:58:58 3
SuperDCA
 
Resource Report
Resource Website
1+ mentions
SuperDCA (RRID:SCR_018175) data analysis software, data processing software, software application, software resource Software tool for global direct coupling analysis of input genome alignments. Implements variant of pseudolikelihood maximization direct coupling analysis, with emphasis on optimizations that enable its use on genome scale. May be used to discover co evolving pairs of loci.Used for genome wide epistasis analysis. Protein, sequence, alignment, analysis, genome, loci, epistasis Academy of Finland ;
European Research Council ;
Royal Society ;
Wellcome Trust
PMID:29813016 Free, Available for download, Freely available SCR_018175 Super Direct Coupling Analysis 2026-09-12 12:58:58 1
genomics resource for animal lectins
 
Resource Report
Resource Website
1+ mentions
genomics resource for animal lectins (RRID:SCR_018122) data or information resource, portal, topical portal Resource presents information about animal lectins involved in various sugar recognition processes. Genomic, animal lectin, sugar recognition process has parent organization: Imperial College London; London; United Kingdom BBSRC ;
Consortium for Functional Glycomics ;
Wellcome Trust
Free, Freely available SCR_018122 2026-09-12 12:58:57 3
GOtcha
 
Resource Report
Resource Website
1+ mentions
GOtcha (RRID:SCR_005790) GOtcha analysis service resource, data analysis service, production service resource, service resource GOtcha provides a prediction of a set of GO terms that can be associated with a given query sequence. Each term is scored independently and the scores calibrated against reference searches to give an accurate percentage likelihood of correctness. These results can be displayed graphically. Why is GOtcha different to what is already out there and why should you be using it? * GOtcha uses a method where it combines information from many search hits, up to and including E-values that are normally discarded. This gives much better sensitivity than other methods. * GOtcha provides a score for each individual term, not just the leaf term or branch. This allows the discrimination between confident assignments that one would find at a more general level and the more specific terms that one would have lower confidence in. * The scores GOtcha provides are calibrated to give a real estimate of correctness. This is expressed as a percentage, giving a result that non-experts are comfortable in interpreting. * GOtcha provides graphical output that gives an overview of the confidence in, or potential alternatives for, particular GO term assignments. The tool is currently web-based; contact David Martin for details of the standalone version. Platform: Online tool function, protein, prediction, genome, annotation, gene, statistical analysis is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: University of Dundee; Scotland; United Kingdom
Wellcome Trust 060269;
European Union fifth framework QLRI-CT-2000-00127
PMID:15550167 Free for academic use nlx_149269 http://www.compbio.dundee.ac.uk/Software/GOtcha/gotcha.html SCR_005790 2026-09-12 01:01:39 3
Expression Profiler
 
Resource Report
Resource Website
1+ mentions
Expression Profiler (RRID:SCR_005821) Expression Profiler analysis service resource, data analysis service, production service resource, service resource THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The EP:GO browser is built into EBI's Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice. other analysis, cluster, analysis, visualization, gene expression, genomic, gene ontology, gene association, microarray, protein-protein interaction, gene, bio.tools is listed by: Gene Ontology Tools
is listed by: Debian
is listed by: bio.tools
is related to: Gene Ontology
has parent organization: European Bioinformatics Institute
European Union ;
Wellcome Trust ;
Estonian Science Foundation 5724;
Estonian Science Foundation 5722
PMID:15215431 THIS RESOURCE IS NO LONGER IN SERVICE biotools:expression_profiler, nlx_149323 https://bio.tools/expression_profiler SCR_005821 Expression Profiler at the EBI 2026-09-12 01:01:39 6
FunTree
 
Resource Report
Resource Website
1+ mentions
FunTree (RRID:SCR_006014) FunTree data or information resource, database FunTree provides a range of data resources to detect the evolution of enzyme function within distant structurally related clusters within domain super families as determined by CATH. To access the resource enter a specific CATH superfamily code or search for a structure / sequence / function (either via a EC code or KEGG ligand / reaction ID, PDB ID or UniProtKB ID). Or browse the resource via superfamily / function / structure / metabolites & reactions via the menu on the left panel. FunTree is a new resource that brings together sequence, structure, phylogenetic, chemical and mechanistic information for structurally defined enzyme superfamilies. Gathering together this range of data into a single resource allows the investigation of how novel enzyme functions have evolved within a structurally defined superfamily as well as providing a means to analyse trends across many superfamilies. This is done not only within the context of an enzyme''''s sequence and structure but also the relationships of their reactions. Developed in tandem with the CATH database, it currently comprises 276 superfamilies covering 1800 (70%) of sequence assigned enzyme reactions. Central to the resource are phylogenetic trees generated from structurally informed multiple sequence alignments using both domain structural alignments supplemented with domain sequences and whole sequence alignments based on commonality of multi-domain architectures. These trees are decorated with functional annotations such as metabolite similarity as well as annotations from manually curated resources such the catalytic site atlas and MACiE for enzyme mechanisms. enzyme function, enzyme superfamily, enzyme, sequence, structure, phylogenetic, chemical, mechanistic, functional annotation, superfamily, gold standard, bio.tools is listed by: Debian
is listed by: bio.tools
is related to: CATH: Protein Structure Classification
is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
is related to: KEGG
is related to: UniProtKB
has parent organization: European Bioinformatics Institute
European Molecular Biology Laboratory; Heidelberg; Germany ;
BBSRC ;
Wellcome Trust 081989/Z/07/A;
DOE contract DE-AC02-06CH11357
PMID:22006843 Free biotools:funtree, nlx_151402 https://bio.tools/funtree SCR_006014 2026-09-12 01:01:40 4

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