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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
GOTrack
 
Resource Report
Resource Website
1+ mentions
GOTrack (RRID:SCR_016399) web service, data or information resource, data access protocol, software resource, database Open source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis. database, system, access, historical, monitor, record, gene, genomic, data, analysis, ontology, annotation, bioinformatics is listed by: OMICtools
is related to: University of British Columbia; British Columbia; Canada
NIH MH111099;
NSERC Discovery Grant ;
Canadian Foundation for Innovation infrastructure ;
CIHR
DOI:10.1101/320861 Free, Available for download, Freely available https://github.com/PavlidisLab/gotrack
https://omictools.com/gotrack-tool
SCR_016399 2026-02-14 02:03:12 1
HOMOZYGOSITYMAPPER
 
Resource Report
Resource Website
100+ mentions
HOMOZYGOSITYMAPPER (RRID:SCR_001714) HomozygosityMapper data analysis service, production service resource, service resource, analysis service resource A web-based approach of homozygosity mapping that can handle tens of thousands markers. User can upload their own SNP genotype files to the database. Intuitive graphic interface is provided to view the homozygous stretches, with the ability of zooming into single chromosomes or user-defined chromosome regions. The underlying genotypes in all samples are displayed. The software is also integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. (entry from Genetic Analysis Software) gene, genetic, genomic, perl, genotype, homozygosity score, homozygosity, bio.tools, FASEB list is listed by: OMICtools
is listed by: Genetic Analysis Software
is listed by: bio.tools
is listed by: Debian
has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany
PMID:19465395 Free, Freely Available nlx_154069, biotools:homozygositymapper, OMICS_00123 https://bio.tools/homozygositymapper SCR_001714 2026-02-14 02:06:03 121
MADELINE
 
Resource Report
Resource Website
1+ mentions
MADELINE (RRID:SCR_001979) MADELINE software resource, service resource, software application Software tool designed for preparing, visualizing, and exploring human pedigree data used in genetic linkage studies. It converts pedigree and marker data into formats required by popular linkage analysis packages, provides powerful ways to query pedigree data sets, and produces Postscript pedigree drawings that are useful for rapid data review. gene, genetic, genomic, c, unix, solaris, freebsd, openbsd, macos, ms-windows, cygwin, linux, pedigree, draw, linkage association, family association is listed by: OMICtools
is listed by: Genetic Analysis Software
has parent organization: University of Michigan; Ann Arbor; USA
PMID:17488757 THIS RESOURCE IS NO LONGER IN SERVICE nlx_154446, OMICS_00210 http://eyegene.ophthy.med.umich.edu/#madeline SCR_001979 Madeline 2026-02-14 02:06:06 5
Phevor
 
Resource Report
Resource Website
1+ mentions
Phevor (RRID:SCR_002273) Phevor data analysis service, production service resource, service resource, analysis service resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. Tool that integrates phenotype, gene function, and disease information with personal genomic data for improved power to identify disease-causing alleles. It works by combining knowledge resident in multiple biomedical ontologies with the outputs of variant prioritization tools. It does so using an algorithm that propagates information across and between ontologies. This process enables Phevor to accurately reprioritize potentially damaging alleles identified by variant prioritization tools in light of gene function, disease, and phenotype knowledge. Phevor is especially useful for single exome and family trio-based diagnostic analyses, the most commonly occurring clinical scenarios, and ones for which existing personal-genomes diagnostic tools are most inaccurate and underpowered. Phevor not only improves diagnostic accuracy for individuals presenting with established disease phenotypes, but also for those with previously undescribed and atypical disease presentations. Importantly, Phevor is not limited to known diseases, or known disease-causing alleles. genome interpretation, variant prioritization, disease gene prioritization, phenotype, gene function, disease, genomic, disease-causing allele, gene, function, allele has parent organization: University of Utah School of Medicine; Utah; USA PMID:24702956 THIS RESOURCE IS NO LONGER IN SERVICE SciRes_000139 SCR_002273 Phenotype Driven Variant Ontological Re-Ranking Tool 2026-02-14 02:06:06 9
AceView
 
Resource Report
Resource Website
100+ mentions
AceView (RRID:SCR_002277) AceView/WormGenes data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented August 29, 2016. AceView offers an integrated view of the human, nematode and Arabidopsis genes reconstructed by co-alignment of all publicly available mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable up-to-date resource on the genes and their functions and to stimulate further validating experiments at the bench. AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals' transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm. In this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated. Our goals are to offer an up-to-date resource on the genes, in the hope to stimulate further experiments at the bench, or to help medical research. AceView can be queried by meaningful words or groups of words as well as by most standard identifiers, such as gene names, Entrez Gene ID, UniGene ID, GenBank accessions. est, exon, expression, function, gene, alignment, arabidopsis, cdna, co-alignment, coding, disease, genome, genomic, human, intron, localization, mammal, mouse, mrna, nematode, pathway, phenotype, plant, polyadenylation, promoter, rat, sequence, signal, tissue, transcript, transcriptome, worm, blast, gold standard has parent organization: NCBI THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-21007, r3d100010651 https://doi.org/10.17616/R3260G http://www.ncbi.nih.gov/IEB/Research/Acembly/ SCR_002277 AceView genes, AceView/WormGenes, The AceView Genes 2026-02-14 02:05:39 186
DogMap
 
Resource Report
Resource Website
DogMap (RRID:SCR_002332) data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. An international collaboration between 46 labs from 20 different countries towards a low resolution canine marker map under the auspices of the International Society for Animal Genetics (ISAG). The map under development should achieve a resolution of about 20 cM and some of the markers should be mapped physically. The participants have agreed to use microsatellites as markers on a common panel of reference families which will provide the backbone of the marker map. It is foreseen to also include type I markers in the mapping effort and to produce cosmid derived microsatellites for physical mapping. For this purpose part of the effort focuses on the standardization of the canine karyotype. Special attention is payed to hereditary diseases where efforts are under way to establish resource families either by collecting families or by specific breeding. A point of emphasis of the DogMap project is the setting up of an internationally accessible database for handling the mapping data. The structure of the DogMap collaboration includes a managing committee and scientific advisers. The managing committee is responsible for the overall coordination of the activities within the collaboration, for the dissemination of relevant information to all of the participants and for the representation of DogMap outside the collaboration., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. family, genetic, animal, breeding, canine, development, disease, dog, genomic, hereditary, karyotype, map, mapping, marker, microsatellite, model organisms and comparative genomics databases, physical has parent organization: University of Basel; Basel; Switzerland THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-21123 SCR_002332 DogMap 2026-02-14 02:06:06 0
Full-Malaria: Malaria Full-Length cDNA Database
 
Resource Report
Resource Website
1+ mentions
Full-Malaria: Malaria Full-Length cDNA Database (RRID:SCR_002348) data or information resource, database FULL-malaria is a database for a full-length-enriched cDNA library from the human malaria parasite Plasmodium falciparum. Because of its medical importance, this organism is the first target for genome sequencing of a eukaryotic pathogen; the sequences of two of its 14 chromosomes have already been determined. However, for the full exploitation of this rapidly accumulating information, correct identification of the genes and study of their expression are essential. Using the oligo-capping method, this database has produced a full-length-enriched cDNA library from erythrocytic stage parasites and performed one-pass reading. The database consists of nucleotide sequences of 2490 random clones that include 390 (16%) known malaria genes according to BLASTN analysis of the nr-nt database in GenBank; these represent 98 genes, and the clones for 48 of these genes contain the complete protein-coding sequence (49%). On the other hand, comparisons with the complete chromosome 2 sequence revealed that 35 of 210 predicted genes are expressed, and in addition led to detection of three new gene candidates that were not previously known. In total, 19 of these 38 clones (50%) were full-length. From these observations, it is expected that the database contains approximately 1000 genes, including 500 full-length clones. It should be an invaluable resource for the development of vaccines and novel drugs. Full-malaria has been updated in at least three points. (i) 8934 sequences generated from the addition of new libraries added so that the database collection of 11,424 full-length cDNAs covers 1375 (25%) of the estimated number of the entire 5409 parasite genes. (ii) All of its full-length cDNAs and GenBank EST sequences were mapped to genomic sequences together with publicly available annotated genes and other predictions. This precisely determined the gene structures and positions of the transcriptional start sites, which are indispensable for the identification of the promoter regions. (iii) A total of 4257 cDNA sequences were newly generated from murine malaria parasites, Plasmodium yoelii yoelii. The genome/cDNA sequences were compared at both nucleotide and amino acid levels, with those of P.falciparum, and the sequence alignment for each gene is presented graphically. This part of the database serves as a versatile platform to elucidate the function(s) of malaria genes by a comparative genomic approach. It should also be noted that all of the cDNAs represented in this database are supported by physical cDNA clones, which are publicly and freely available, and should serve as indispensable resources to explore functional analyses of malaria genomes. Sponsors: This database has been constructed and maintained by a Grant-in-Aid for Publication of Scientific Research Results from the Japan Society for the Promotion of Science (JSPS). This work was also supported by a Special Coordination Funds for Promoting Science and Technology from the Science and Technology Agency of Japan (STA) and a Grant-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Science, Sports and Culture of Japan. drug, eukaryotic, expression, function, gene, alignment, amino acid, cdna, chromosome, clone, coding, comparative, genome, genomic, human, malaria, medical, nucleotide, oligo-capping, organism, parasite, pathogen, physical, plasmodium falciparum, promoter, protein, region, sequence, sequencing, unicellular eukaryote genome databases, vaccine has parent organization: University of Tokyo; Tokyo; Japan PMID:18987005
PMID:14681428
nif-0000-21157 SCR_002348 Full-Malaria 2026-02-14 02:05:47 2
Ancestrymap
 
Resource Report
Resource Website
10+ mentions
Ancestrymap (RRID:SCR_004353) ANCESTRYMAP software resource, source code, software application Software application that finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans. It can be downloaded for either UNIX or Linux. disease gene, ancestry, gene, genomic, unix, linux, admixture mapping, admixture, genome, linkage disequilibrium, population is listed by: OMICtools
is listed by: Genetic Analysis Software
is listed by: bio.tools
has parent organization: Harvard Medical School; Massachusetts; USA
Burroughs Wellcome Fund ;
NHGRI K-01 HG002758-01
PMID:15088269 Restricted nlx_39116, biotools:ancestrymap, OMICS_02083 https://reich.hms.harvard.edu/software
https://bio.tools/ancestrymap
http://genepath.med.harvard.edu/~reich/Software.htm, http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html SCR_004353 2026-02-14 02:05:47 12
Forsyth Institute Bioinformatics Core Facility
 
Resource Report
Resource Website
Forsyth Institute Bioinformatics Core Facility (RRID:SCR_009783) core facility, access service resource, service resource Core specializes in oral microbial genomics, taxonomy, phylogenetics and the next generation sequence (NGS) data analysis with both in house and cloud high performance computational resource. In addition to supporting funded bioinformatics projects, Bioinformatics Core will also provide computational support to Forsyth and other researchers for processing, analyzing, and interpreting biological data. USEDit, ABRF, microarray, data analysis service, microbial, genomic, gene expression, biological data is listed by: Eagle I
is listed by: ABRF CoreMarketplace
has parent organization: Forsyth Institute
open SCR_021784, nlx_156252, ABRF_1234 https://coremarketplace.org/?FacilityID=1234 http://harvard.eagle-i.net/i/0000012e-6d1b-f8ef-55da-381e80000000 SCR_009783 Forsyth Bioinformatics Core, Forsyth Bioinformatics Core Facility 2026-02-14 02:07:28 0
Harvest-tools
 
Resource Report
Resource Website
1+ mentions
Harvest-tools (RRID:SCR_016132) software resource, software toolkit Software tools archiving and postprocessing for reference-compressed genomic multi-alignments. It is used for creating and interfacing with Gingr files, which are archives that the Harvest Suite uses to store reference-compressed multi-alignments, phylogenetic trees, filtered variants and annotations. archiving, postprocessing, reference, compressed, genomic, multialignment, create, interface, Gingr, file, phylogentic, tree, annotation, bioinformatic, format is listed by: Debian
is listed by: OMICtools
Department of Homeland Security Science and Technology Directorate PMID:25410596 Free, Available for download, Freely available OMICS_08468 https://github.com/marbl/harvest-tools
https://sources.debian.org/src/harvest-tools/
SCR_016132 2026-02-14 02:07:22 4
Sequence Search and Alignment by Hashing Algorithm
 
Resource Report
Resource Website
1+ mentions
Sequence Search and Alignment by Hashing Algorithm (RRID:SCR_000544) SSAHA2 software resource, source code A program designed for the efficient mapping of sequence reads onto genomic references. The software is capable of reading most sequencing platforms and giving a range of outputs are supported. sequence, genomic, analysis, search, alignment, algorithm, mapping, bio.tools is listed by: OMICtools
is listed by: bio.tools
is related to: SMALT
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
PMID:11591649 THIS RESOURCE IS NO LONGER IN SERVICE biotools:ssaha2, OMICS_00690, nlx_93831 https://bio.tools/ssaha2 SCR_000544 ssaha2, ssaha, Sequence Search and Alignment by Hashing Algorithm 2026-02-14 02:07:17 6
Georgia Genomics and Bioinformatics Core at the University of Georgia
 
Resource Report
Resource Website
50+ mentions
Georgia Genomics and Bioinformatics Core at the University of Georgia (RRID:SCR_010994) GGBC training service resource, core facility, access service resource, service resource Core laboratory for nucleic acid sequencing and bioinformatics. Used for research support, education, and training. Services include genomic techniques and applications, sequencing technologies, and bioinformatics analyses, writting letters of support for grant applications submitted to funding agencies. GGBC operates multiple platforms for short-, long-, and single-molecule sequencing reads (i.e., Illumina MiSeq and NextSeq, PacBio Sequel, and Oxford Nanopore MinIon). nucleic, acid, sequencing, labs, analysis, equipment, genomic, technique, analysis, grant, application is listed by: ScienceExchange
is related to: University of Georgia Labs and Facilities
has parent organization: University of Georgia; Georgia; USA
SciEx_9234 http://www.scienceexchange.com/facilities/georgia-genomics-facility-uga, http://www.scienceexchange.com/facilities/georgia-genomics-facility-uga SCR_010994 Georgia Genomics & Bioinformatics Core, Georgia Genomics and Bioinformatics Core at UGA, University of Georgia Genomics Facility, Georgia Genomics and Bioinformatics Core 2026-02-14 02:08:20 71
FASTLINK
 
Resource Report
Resource Website
50+ mentions
FASTLINK (RRID:SCR_009177) FASTLINK software resource, software application Software application (entry from Genetic Analysis Software) gene, genetic, genomic, c, unix, vms, ms-dos, .. and can also run in parallel on shared memory unix machines is listed by: Genetic Analysis Software
is listed by: Debian
is listed by: OMICtools
PMID:8807326 OMICS_28405, nlx_154309 https://sources.debian.org/src/fastlink/ SCR_009177 faster version of LINKAGE LINKAGE 2026-02-14 02:06:46 58
FASTEHPLUS
 
Resource Report
Resource Website
FASTEHPLUS (RRID:SCR_009176) FASTEHPLUS software resource, software application THIS RESOURCE IS NO LONGER IN SERVCE, documented September 7, 2016. gene, genetic, genomic, c, ms-windows, unix, dec, osf, solaris is listed by: Genetic Analysis Software THIS RESOURCE IS NO LONGER IN SERVICE nlx_154308 http://www.mrc-epid.cam.ac.uk/Personal/jinghua.zhao/software/ SCR_009176 EHPLUS, faster EH-PLUS EH 2026-02-14 02:07:14 0
ERPA
 
Resource Report
Resource Website
1+ mentions
ERPA (RRID:SCR_009173) ERPA software resource, software application THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application for non-parametric analysis (entry from Genetic Analysis Software) gene, genetic, genomic, c, ms-dos is listed by: Genetic Analysis Software THIS RESOURCE IS NO LONGER IN SERVICE nlx_154302 SCR_009173 Extended Relative Pair Analysis 2026-02-14 02:06:46 7
EXOMEPICKS
 
Resource Report
Resource Website
1+ mentions
EXOMEPICKS (RRID:SCR_009174) EXOMEPICKS software resource, software application Software application that suggests individuals to be sequenced in a large pedigree. ExomePicks assumes that a genotyping chip or another cost effective means will be used to determine IBD sharing in the pedigree and that, subsequently, one would like to sequence a minimal number of individuals and use their sequences together with IBD information to deduce the sequence of other individuals in the pedigree. We are currently using it in the context of whole exome and whole genome sequencing studies to pick individuals to be sequenced from large family collections. (entry from Genetic Analysis Software) gene, genetic, genomic, bio.tools is listed by: Genetic Analysis Software
is listed by: bio.tools
is listed by: Debian
nlx_154306, biotools:exomepicks https://bio.tools/exomepicks SCR_009174 2026-02-14 02:07:09 6
EMLD
 
Resource Report
Resource Website
1+ mentions
EMLD (RRID:SCR_009171) EMLD software resource, software application Software application to calculate pair-wise linkage disequilibrium based on SNP genotype data from unrelated individuals. EM algorithm is used to estimate pair-wise haplotype frequencies. The output file is in the format of input file for GOLD program, thus it can be directly plug into GOLD to get LD plots. (entry from Genetic Analysis Software) gene, genetic, genomic, java, unix, ms-windows is listed by: Genetic Analysis Software nlx_154298 http://epi.mdanderson.org/~qhuang/Software/pub.htm SCR_009171 EM estimation of haplotype frequencies and LD calculation 2026-02-14 02:07:00 4
EPDT
 
Resource Report
Resource Website
1+ mentions
EPDT (RRID:SCR_009172) EPDT software resource, software application THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application that for detecting linkage/disequilibrium signals # between genetic markers and disease loci, particularly if only one # or a few large pedigrees are available. The strategy differs from # conventional approaches that require at least a moderate number of # families to attain adequate statistical power. The proposed testing # procedure is advantageous in that it provides high statistical power # coupled with reduced sample collection. Furthermore, the proposed # method avoids problems such as potential population stratification # and genetic heterogeneity, and is robust with respect to misspecification # of phenotype. (entry from Genetic Analysis Software) gene, genetic, genomic, unix is listed by: Genetic Analysis Software THIS RESOURCE IS NO LONGER IN SERVICE nlx_154301 SCR_009172 Extended Pedigree Disequilibrium Test 2026-02-14 02:07:14 1
EH
 
Resource Report
Resource Website
EH (RRID:SCR_009168) EH software resource, software application Software application (entry from Genetic Analysis Software) gene, genetic, genomic, pascal, ms-dos, unix is listed by: Genetic Analysis Software nlx_154291 SCR_009168 FASTEHPLUS, EHP, Estimating Haplotype-frequencies EHPLUS 2026-02-14 02:07:14 0
EAGLET
 
Resource Report
Resource Website
1+ mentions
EAGLET (RRID:SCR_009166) EAGLET software resource, software application THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software package that provides a number of improved statistics for detecting linkage and estimating trait location. EAGLET uses multiple subsamples of dense SNP data to detect linkage with increased power, and to construct sharp 95% confidence intervals for the true trait location. gene, genetic, genomic, perl, c, linux, macos is listed by: Genetic Analysis Software THIS RESOURCE IS NO LONGER IN SERVICE nlx_154288 SCR_009166 Efficient Analysis of Genetic Linkage: Testing and Estimation 2026-02-14 02:07:08 1

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