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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 Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Bowtie 2
 
Resource Report
Resource Website
1000+ mentions
Bowtie 2 (RRID:SCR_016368) alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method. sequence, analysis, long, reference, sequence, read, alignment, gap, local, pair, end, rna, rnaseq, bio.tools is used by: HLA-HD
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
is related to: Bowtie
NHGRI R01 HG006102;
NIGMS R01 GM083873
PMID:22388286 Free, Available for download, Freely available biotools:bowtie2 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml, https://github.com/BenLangmead/bowtie2, https://bio.tools/bowtie2 SCR_016368 , bowtie 2, bowtie2 v 2.2.3 2026-09-05 06:27:50 1993
Hypermut
 
Resource Report
Resource Website
100+ mentions
Hypermut (RRID:SCR_014933) data analysis software, data processing software, sequence analysis software, software application, software resource, web application Web application for the analysis and detection of APOBEC-induced hypermutations. The first sequence in the input alignment will be used as the reference sequence, and each of the other sequences will be used as a query sequence. mutation, hypermutation, sequence, sequence analysis software genome, web application PMID:10869039 SCR_014933 Hypermut 2.0 2026-09-05 06:27:52 130
Seq-Gen
 
Resource Report
Resource Website
100+ mentions
Seq-Gen (RRID:SCR_014934) simulation software, software application, software resource Software program that simulates the evolution of nucleotide or amino acid sequences along a phylogeny using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. simulator, simulation software, molecular evolution, nucleotide, amino acid, sequence, phylogeny, phylogenetic tree is listed by: Debian
is listed by: OMICtools
has parent organization: University of Edinburgh; Scotland; United Kingdom
Wellcome Trust ;
BBSRC ;
Fogarty ;
The Royal Society
DOI:10.1093/bioinformatics/13.3.235 Available for download OMICS_15373 https://sources.debian.org/src/seq-gen/ SCR_014934 2026-09-05 06:27:52 158
HCV Sequence Database
 
Resource Report
Resource Website
10+ mentions
HCV Sequence Database (RRID:SCR_006019) HCV Sequence Database analysis service resource, data analysis service, data or information resource, database, production service resource, service resource The HCV sequence database collects and annotates sequence data and provides them to the public via a website that contains a user-friendly search interface and a large number of sequence analysis tools, based on the model of the highly regarded Los Alamos HIV database. The hepatitis C virus (HCV) is a significant threat to public health worldwide. The virus is highly variable and evolves rapidly, making it an elusive target for the immune system and for vaccine and drug design. At present, some 30 000 HCV sequences have been published. This central website provides annotated sequences and analysis tools that will be helpful to HCV scientists worldwide. Things you can do: * Find sequences in the database * Download sequences from the database * Retrieve data about the sequences * Analyze sequences * Work with the sequences using our tools * Download ready-made alignments The HCV sequence database was officially launched in September 2003. Since then, its usage has steadily increased and is now at an average of approximately 280 visits per day from distinct IP addresses. hepatitis c virus, sequence, annotation has parent organization: HCV Databases Hepatitis C NIAID PMID:15377502 Public nlx_151411 SCR_006019 Hepatitis C Sequence Database, Hepatitis C Virus Sequence Database, Los Alamos hepatitis C sequence database 2026-09-05 06:25:45 19
CMHD - Centre for Modeling Human Disease
 
Resource Report
Resource Website
10+ mentions
CMHD - Centre for Modeling Human Disease (RRID:SCR_006101) CMHD analysis service resource, biomaterial manufacture, data or information resource, database, material service resource, production service resource, service resource Multidisciplinary collaboration undertaking genome-wide mutagenesis to functionally annotate the mouse genome and develop new mouse models relevant to human disease. To achieve these goals two major research platforms are carried out: Gene trapping and ENU Mutagenesis. A new challenge is faced in the post-genomic era - the assignment of biological function to the human genome sequence and projecting that assignment into understanding of human health and disease. The Centre for Modeling Human Disease (CMHD) was established to take part in the worldwide initiative to address these challenges. At the CMHD, two fundamentally different, yet complimentary methods are employed to generate mutant mouse models of human disease: chemical mutagenesis by ethylnitrosourea (ENU), and gene trap insertional mutagenesis. The Centre contributes its resources to similar international efforts and is the first of its kind in Canada. The Center is also actively developing other mutagenic strategies including pharmacologic and genetic modifier screens to dissect disease pathways, and novel mutagenic techniques using embryonic stem cells. ENU Database * Statistics for Mouse Physiological Parameters * Search Mutants by Phenotype * Search Mutants by Heritability Gene Trap Database * Search by in vitro Expression Pattern * Search by Gene Trap Sequences CMHD Members Only (must register and login) * Search Mouse Line * Histopathology * Sperm, Tissue, Slide Archiving * CMHD Database Download CMHD Services * Phenotyping * Genetic Mapping * Pathology * Pathology Service Charges mutant, mouse model, chemical mutagenesis, ethylnitrosourea, gene trap insertion, mutagenesis, genome-wide mutagenesis, mouse genome, genome, phenotype, heritability, expression pattern, sequence, image, neurobiology, behavior, embryonic stem cell, gene trapping, enu mutagenesis, human disease has parent organization: Toronto Centre for Phenogenomics
is parent organization of: Centre for Modeling Human Disease Gene Trap Resource
Human disease CIHR ;
Genome Canada
Non-CMHD users are required to register and log in only if you wish to view images on our mouse models. nlx_151636 SCR_006101 Centre for Modeling Human Disease 2026-09-05 06:25:47 12
PRED-GPCR
 
Resource Report
Resource Website
1+ mentions
PRED-GPCR (RRID:SCR_006196) PRED-GPCR analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource A prediction tool for GPCR Family Classification from sequence alone based on a probabilistic method that uses family-specific profile Hidden Markov Models. The PRED-GPCR system is based on a probabilistic method that uses family specific profile HMMs in order to determine to which GPCR family a query sequence belongs or resembles. The approach proposed in this method exploits the descriptive power of profile HMMs along with an exhaustive discrimination assessment method to select only highly selective and sensitive profiles, for each family. The collection of these profiles constitutes a signature library, which is scanned, for significant matches with a given query sequence. The output report for a query sequence consists of two sections: * A ranked list of the profile HMM matches, below the selected individual motif E-value cutoff, along with their corresponding family. * A ranked list of the Combined P-values, E-values as well as the number of profiles matched for each family. To cross-evaluate your results you can browse through Swiss-Prot, Trembl, Pfam and Prosite family related entries. g-protein coupled receptor, classification, hidden markov model, sequence, fasta, family classification, motif, bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: University of Athens Biophysics and Bioinformatics Laboratory
PMID:15215415 nlx_151741, biotools:pred-gpcr https://bio.tools/pred-gpcr SCR_006196 PRED-GPCR: GPCRs Family classification from sequence alone 2026-09-05 06:25:48 2
Generate Pseudo-Random Numbers
 
Resource Report
Resource Website
1+ mentions
Generate Pseudo-Random Numbers (RRID:SCR_006535) data or information resource, portal, topical portal This module implements pseudo-random number generators for various distributions. For integers, uniform selection from a range. For sequences, uniform selection of a random element, a function to generate a random permutation of a list in-place, and a function for random sampling without replacement. On the real line, there are functions to compute uniform, normal (Gaussian), lognormal, negative exponential, gamma, and beta distributions. For generating distributions of angles, the von Mises distribution is available. Sponsors: This resource is supported by ASTi logo Advanced Simulation Technology Inc. (ASTi); Array BioPharma Inc.; BizRate.com; Canonical Ltd.; CCP Games; cPacket Networks; EarnMyDegree.com; Enthought Inc.; Exoweb Ltd.; Google; HitMeister Inc.; IronPort Systems; KNMP; Lucasfilm; Madison Tyler LLC.; Merfin, LLC.; Microsoft; OpenEye Scientific Software; Opsware, Inc.; O''Reilly & Associates, Inc.; PropertySold.ca; Rogue Wave; SEO Moves; Strakt Holdings, Inc.; Sun Microsystems; Tabblo; ZeOmega, LLC., and Zope Corporation. element, function, generator, computation, distribution, integer, lognormal, module, number, pseudo-random, range, sampling, sequence nif-0000-30012 http://docs.python.org/lib/module-random.html SCR_006535 Generate Pseudo 2026-09-05 06:25:56 1
Rat Genome Database (RGD)
 
Resource Report
Resource Website
100+ mentions
Rat Genome Database (RGD) (RRID:SCR_006444) RGD data or information resource, data repository, database, service resource, storage service resource Database for genetic, genomic, phenotype, and disease data generated from rat research. Centralized database that collects, manages, and distributes data generated from rat genetic and genomic research and makes these data available to scientific community. Curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data is provided. Facilitates investigators research efforts by providing tools to search, mine, and analyze this data. Strain reports include description of strain origin, disease, phenotype, genetics, immunology, behavior with links to related genes, QTLs, sub-strains, and strain sources. RIN, Resource Information Network, mouse, rat, human, gene, qtl, marker, map, strain, sequence, est, genome, ontology, pathway, comparative genomics, physiology, phenotype, disease, model organism, proteomics, function, genetic, genomic, variation, immunology, behavior, knockout, inbred rat strain, mutant, congenic rat, recombinant inbred rat, data analysis service, organism supplier, genotype, gold standard, FASEB list, RRID Community Authority uses: InterMOD
is used by: ChannelPedia
is used by: Resource Identification Portal
is used by: DisGeNET
is used by: Integrated Animals
is used by: NIH Heal Project
is recommended by: Resource Identification Portal
is listed by: re3data.org
is listed by: InterMOD
is listed by: Resource Information Network
is affiliated with: InterMOD
is related to: Rat Gene Symbol Tracker
is related to: MPO
is related to: NIF Data Federation
is related to: MONARCH Initiative
is related to: Vertebrate Trait Ontology
is related to: Biositemaps
is related to: One Mind Biospecimen Bank Listing
is related to: AmiGO
is related to: OMICtools
is related to: re3data.org
is related to: Integrated Manually Extracted Annotation
is related to: OntoMate
has parent organization: Medical College of Wisconsin; Wisconsin; USA
is parent organization of: Diabetes Disease Portal
is parent organization of: Rat Strain Ontology
is parent organization of: Rat Strain Ontology
is parent organization of: Renal Disease Portal
is organization facet of: Alliance of Genome Resources
NHLBI PMID:23434633
PMID:18996890
PMID:17151068
Free, Freely available nif-0000-00134, r3d100010417, OMICS_01660 https://doi.org/10.17616/R3WK60 SCR_006444 , Rat Genome Database, RGD 2026-09-05 06:25:53 280
FlyBase
 
Resource Report
Resource Website
1000+ mentions
FlyBase (RRID:SCR_006549) FB data or information resource, data repository, database, organism-related portal, portal, service resource, storage service resource, topical portal Database of Drosophila genetic and genomic information with information about stock collections and fly genetic tools. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. Additionally, FlyBase accepts data submissions. FlyBase can be searched for genes, alleles, aberrations and other genetic objects, phenotypes, sequences, stocks, images and movies, controlled terms, and Drosophila researchers using the tools available from the "Tools" drop-down menu in the Navigation bar. RIN, Resource Information Network, mutant, gene, genome, blast, genotype, phenotype, allele, sequence, stock, image, movie, controlled term, video resource, image collection, life-cycle, genome, expression, rna-seq, genetics, drosophilidae, bio.tools, FASEB list, RRID Community Authority is used by: NIF Data Federation
is used by: Resource Identification Portal
is used by: PhenoGO
is used by: Integrated Animals
is used by: Drososhare
is recommended by: NIDDK Information Network (dkNET)
is recommended by: National Library of Medicine
is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
is listed by: re3data.org
is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is listed by: Resource Information Network
is related to: FlyMine
is related to: Virtual Fly Brain
is related to: AmiGO
is related to: Drosophila melanogaster Exon Database
is related to: HomoloGene
is related to: UniParc at the EBI
is related to: UniParc
is related to: Gene Ontology
is related to: NIH Data Sharing Repositories
is related to: GBrowse
is related to: Integrated Manually Extracted Annotation
is related to: PhenoGO
has parent organization: Harvard University; Cambridge; United States
has parent organization: University of Cambridge; Cambridge; United Kingdom
has parent organization: Indiana University; Indiana; USA
has parent organization: University of New Mexico; New Mexico; USA
is parent organization of: Drosophila anatomy and development ontologies
is parent organization of: Fly Taxonomy
is parent organization of: FlyBase Controlled Vocabulary
is parent organization of: Drosophila Development Ontology
is organization facet of: Alliance of Genome Resources
Indiana Genomics Initiative ;
MRC ;
NIH Blueprint for Neuroscience Research ;
NIHGRI P41 HG000739;
NSF
PMID:24234449
PMID:22127867
PMID:18948289
PMID:18641940
PMID:18160408
PMID:17099233
PMID:16381917
PMID:15608223
PMID:12519974
PMID:11752267
PMID:11465064
PMID:9847148
PMID:9399806
PMID:9045212
PMID:8594600
PMID:8578603
PMID:7937045
PMID:7925011
nif-0000-00558, r3d100010591, OMICS_01649, biotools:flybase https://bio.tools/flybase, https://doi.org/10.17616/R3903Q http://flybase.net SCR_006549 flybase A Drosophila Genomic and Genetic Database, FlyBase: A Database of Drosophila Genes and Genomes, FLYBASE, FlyBase: A Database of Drosophila Genes & Genomes, FB 2026-09-05 06:25:56 4234
miRDeep
 
Resource Report
Resource Website
100+ mentions
miRDeep (RRID:SCR_010829) miRDeep2 data analysis software, data processing software, sequence analysis software, software application, software resource Software tool to identify known and novel miRNA genes in seven animal clades by analyzing sequenced RNAs. Used for discovering known and novel miRNAs from small RNA sequencing data. miRNA, gene, animal, clade, analysis, sequence, RNA, data is listed by: OMICtools China Scholarship Council ;
German Ministry of Education and Research ;
Helmholtz Association ;
Helmholtz-Alliance on Systems Biology ;
Max Delbrück Centrum Systems Biology Network ;
Senate of Berlin
PMID:18392026
PMID:21911355
Free, Available for download, Freely available OMICS_00373 https://github.com/rajewsky-lab/mirdeep2 SCR_010829 2026-09-05 06:26:48 182
MacVector
 
Resource Report
Resource Website
1000+ mentions
MacVector (RRID:SCR_015700) data analysis software, data processing software, sequence analysis software, software application, software resource Software application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, agarose gel simulation and a variety of other functions. vector, sequence, sequence alignment, sequence editing, primer design, phylogenetic reconstruction, FASEB list Commercially available, Available for purchase, Runs on Mac OS, Free version available SCR_015700 2026-09-05 06:27:58 1508
Poretools
 
Resource Report
Resource Website
50+ mentions
Poretools (RRID:SCR_015879) data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit Software toolkit for analyzing nanopore sequence data. nanopore, sequence, python, oxford nanopore, MinION, quality control, downstream analysis, bio.tools is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
Medical Research Council ;
NHGRI R01 HG006693
PMID:25143291 Open source, Free, Available for download biotools:poretools https://bio.tools/poretools SCR_015879 2026-09-05 06:28:00 83
Ariba
 
Resource Report
Resource Website
100+ mentions
Ariba (RRID:SCR_015976) data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit Analysis software that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling. software, analysis, tool, sequence, antibiotic, resistance, assembly, local, mlst is listed by: Debian
is listed by: OMICtools
Biotechnology and Biological Sciences Research Council BB/M014088/1;
Wellcome Trust 206194
PMID:29177089
DOI:10.1099/mgen.0.000131
Free, Available for download, Freely available OMICS_17327 https://sources.debian.org/src/artemis/ SCR_015976 2026-09-05 06:28:01 220
Atac
 
Resource Report
Resource Website
1000+ mentions
Atac (RRID:SCR_015980) alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource Alignment analysis software tool for comparative mapping between two genome assemblies or between two different genomes. It can cache intermediate results to speed a comparisons of multiple sequences. software, tool, DNA, sequence, analysis, aligning, genome, compare, mapping, assembly, bio.tools is listed by: Debian
is listed by: bio.tools
is listed by: OMICtools
DOI:10.1093/bioinformatics/btr285 Free, Freely available, Available for download OMICS_29044, biotools:atac https://bio.tools/atac, https://sources.debian.org/src/atac/ SCR_015980 2026-09-05 06:28:01 1826
Axe
 
Resource Report
Resource Website
1+ mentions
Axe (RRID:SCR_015984) data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit Software for sequencing data analysis and demultiplexing. It can be used in situations where sequence reads contain the barcodes that uniquely distinguish samples. software, tool, sequence, analysis, barcode, demultiplexing is listed by: Debian
is listed by: OMICtools
Free, Freely available, Available for download OMICS_19788 https://readthedocs.org/projects/axe-demultiplexer/, https://sources.debian.org/src/baitfisher/ SCR_015984 Axe-demultiplexer 2026-09-05 06:28:02 1
Bamtools
 
Resource Report
Resource Website
100+ mentions
Bamtools (RRID:SCR_015987) data analysis software, data management software, data processing software, software application, software resource, software toolkit Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies. c++, api, sam, bam genome, sequence, alignment, data, analysis, management, command, manipulation, binary, map, bio.tools is listed by: Debian
is listed by: bio.tools
is listed by: OMICtools
NHGRI R01 HG004719;
NHGRI RC2 HG005552
PMID:21493652
DOI:10.1093/bioinformatics/btr174
biotools:bamtools, OMICS_11315 https://bio.tools/bamtools, https://sources.debian.org/src/bamtools/ SCR_015987 API:Application Programming Interface, BAM:Binary Alignment Map, SAM:Sequence Alignment Map 2026-09-05 06:28:02 344
G-Anchor
 
Resource Report
Resource Website
1+ mentions
G-Anchor (RRID:SCR_016046) G-Anchor alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource Software for comparing large genomes and exploiting highly conserved sequences as evolutionary-stable "anchors". The pipeline maps a newly sequenced genome (assembled in scaffolds) on a reference genome without the need of a supercomputer. anchor, comparison, scaffold, whole genome, alignment, sequence, mapping, anchoring, highly conserved elements, hce, evolution Biotechnology and Biological Sciences Research Council BB/J010170/1;
HPC Wales
Free, Available for download SCR_016046 G-Anchor: A novel approach for cross-species comparison 2026-09-05 06:28:02 1
Blixem
 
Resource Report
Resource Website
1+ mentions
Blixem (RRID:SCR_015994) alignment software, data processing software, image analysis software, software application, software resource Software for sequence alignments that displays multiple match sequences aligned against a single genomic reference sequence. It can be used for manipulation, display and annotation of genomic data, to check the quality of an alignment, to find missing/misaligned sequence, and to identify splice sites and polyA sites. software, sequence, alignment, annotation, genomic, reference, data, display, manipulation, DNA is related to: SEQtools
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
NHGRI U54 HG00455;
Wellcome Trust Grant 098051
PMID:26801397 Free, Available for download SCR_015994 SEQtools Blixem 2026-09-05 06:28:02 2
ALTER
 
Resource Report
Resource Website
100+ mentions
ALTER (RRID:SCR_015968) alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource, web application Web application to perform program-oriented conversion of DNA and protein alignments and transform between multiple sequence alignment formats. ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats. Alignment conversion, genome, sequence, DNA, protein, format alignment, phylogenetics, bio.tools is listed by: Debian
is listed by: bio.tools
is listed by: OMICtools
European Research Council ERC-2007-Stg 203161-PHYGENOM to D.P.;
INBIOMED initiative ;
Spanish Ministry of Science and Education BFU2009-08611 to D.P.;
University of Vigo 09VIB10 to F.F-.R.;
Xunta de Galicia PGIDIT07PXIB310202PR to D.P.
PMID:20439312
DOI:10.1093/nar/gkq321
Freely available, Free, Available for download OMICS_19786, biotools:alter https://github.com/sing-group/ALTER, https://bio.tools/alter, https://sources.debian.org/src/alter-sequence-alignment/ SCR_015968 ALTER: ALignment Transformation EnviRonment, ALignment Transformation EnviRonment 2026-09-05 06:28:01 125
AMAP
 
Resource Report
Resource Website
100+ mentions
AMAP (RRID:SCR_015969) alignment software, data processing software, image analysis software, software application, software resource, source code Source code that performs multiple alignment of peptidic sequences. It utilizes posterior decoding and a sequence-annealing alignment, instead of the traditional progressive alignment method. software, peptide, sequence, alignment, annealing, bioinformatics, multiple, svn, posterior, decoding is listed by: Debian
is listed by: OMICtools
has parent organization: University of California at Berkeley; Berkeley; USA
NHGRI R01 HG2362;
NSF CCF0347992;
NSF EF 03-31494
PMID:17237099
DOI:10.1093/bioinformatics/btl311
Free, Available for download OMICS_19787 http://baboon.math.berkeley.edu/amap/, https://sources.debian.org/src/amap-align/ https://sources.debian.org/src/amos-assembler/ SCR_015969 amap-align 2026-09-05 06:28:01 400

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