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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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HiGlass Resource Report Resource Website 10+ mentions |
HiGlass (RRID:SCR_026687) | web application, source code, software resource | Web-based visual exploration and analysis of genome interaction maps. | visual exploration and analysis, genome interaction maps, | NCI U01CA200059; NHGRI R00 HG007583; NHGRI U54 HG007963 |
PMID:30143029 | Free, Available for download, Freely available | SCR_026687 | 2026-02-15 09:23:21 | 45 | |||||||||
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apeglm Resource Report Resource Website |
apeglm (RRID:SCR_026951) | software toolkit, software resource | Software package provides Bayesian shrinkage estimators for effect sizes for variety of GLM models, using approximation of posterior for individual coefficients. | Bayesian shrinkage estimators, | NHGRI R01 HG009125; NCI P01 CA142538; NIEHS P30 ES010126; NIGMS R01 GM070335 |
PMID:30395178 | Free, Available for download, Freely available, | SCR_026951 | , Approximate Posterior Estimation for generalized linear model, Approximate posterior estimation for GLM | 2026-02-15 09:24:04 | 0 | ||||||||
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dREG Resource Report Resource Website 1+ mentions |
dREG (RRID:SCR_027012) | software application, source code, software resource | Software tool for detecting regulatory elements using GRO-seq and PRO-seq. | detecting regulatory elements, GRO-seq, PRO-seq | NHGRI 5R01HG007070; NIDDK R01 DK058110 |
PMID:25799441 | Free, Available for download, Freely available | SCR_027012 | 2026-02-15 09:24:08 | 1 | |||||||||
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PHATE Resource Report Resource Website 1+ mentions |
PHATE (RRID:SCR_027119) | software application, data visualization software, source code, data processing software, software resource, 3d visualization software | Software tool for visualizing high dimensional data using novel conceptual framework for learning and visualizing manifold to preserve both local and global distances. | visualizing high dimensional data, high dimensional data, | NICHD F31HD097958; NHGRI 1R01HG008383; NSF ; NIGMS R01GM107092; NIGMS R01GM130847 |
PMID:31796933 | Free, Available for download, Freely available, | SCR_027119 | Potential of Heat-diffusion for Affinity-based Transition Embedding | 2026-02-15 09:23:30 | 2 | ||||||||
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TEProf3 Resource Report Resource Website |
TEProf3 (RRID:SCR_027288) | source code, software toolkit, software resource | Software pipeline to detect Transposable Elements transcripts. Used to identify TE-derived promoters and transcripts using transcriptomic data from multiple sources, including short-read RNA-seq data, long-read RNA-seq data and single cell RNA-seq data. | Transposable Elements, Transposable Elements transcripts, detect TE transcripts, transcriptomic data, short-read RNA-seq data, long-read RNA-seq data, single cell RNA-seq data, | NHGRI R01HG007175; NIA R01AG078958; NINDS U24NS132103; NHGRI U01HG013227 |
PMID:40360186 | Free, Available for download, Freely available, | SCR_027288 | , TE-derived Promoter Finder 3 | 2026-02-15 09:24:06 | 0 | ||||||||
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Current Topics in Genome Analysis Resource Report Resource Website |
Current Topics in Genome Analysis (RRID:SCR_006475) | CTGA | data or information resource, training resource, topical portal, portal | Current Topics in Genome Analysis lecture series consists of 13 lectures on successive Wednesdays, with a mixture of local and outside speakers covering the major areas of genomics. In this tenth edition of the series, rather than splitting the lectures into laboratory-based and computationally-based blocks, we have intermingled the lectures by general subject area. We hope that this approach conveys the idea that both laboratory- and computationally-based approaches are necessary in order to do cutting-edge biological research in the future. The lectures are geared at the level of first year graduate students, are practical in nature, and are intended for a diverse audience. Handouts will be provided for each lecture, and time will be available at the end of each lecture for questions and discussion. All lectures are held on Wednesday mornings from 9:30 a.m. to 11:00 a.m. in the Lipsett Amphitheatre of the National Institutes of Health Clinical Center (Building 10). Course Directors: Andy Baxevanis, Ph.D., Eric Green, M.D., Ph.D., Tyra Wolfsberg, Ph.D. Lectures in this series will be available on the GenomeTV channel of YouTube viewing shortly after the live lecture and also includes all of the handouts. Lectures will not be Webcast live. The lecture series archives (available from 2005-) covers important milestones in genetics. CME Credits: This activity has been approved for AMA PRA Category 1 Credits. The intended audience includes clinicians, clinical geneticists, social and behavioral scientists, genetic counselors, those involved with genetics and public policy, health educators, and other biomedical and clinical scientists with an interest in genetics, genomics and personalized medicine. No prior expertise on the part of the audience will be required and the lecturers will be instructed to provide any relevant background as part of their lectures. | genomics, bioinformatics, lecture, genome analysis | has parent organization: National Human Genome Research Institute | NHGRI | http://www.genome.gov/COURSE2012 | SCR_006475 | Current Topics in Genome Analysis 2012, Current Topics in Genome Analysis lecture series, NHGRI: Current Topics in Genome Analysis | 2026-02-15 09:19:18 | 0 | |||||||
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scHiCluster Resource Report Resource Website |
scHiCluster (RRID:SCR_027854) | software toolkit, software resource | Software Python package for single-cell chromosome contact data analysis. It includes the identification of cell types (clusters), loop calling in cell types, and domain and compartment calling in single cells. Facilitates visualization and comparison of single-cell 3D genomes. | single-cell chromosome contact data analysis, single-cell, chromosome, contact, data analysis, | NHGRI R21 HG009274 | PMID:31235599 | Free, Available for download, Freely Available | SCR_027854 | 2026-02-15 09:24:18 | 0 | |||||||||
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PHAST Resource Report Resource Website 50+ mentions |
PHAST (RRID:SCR_003204) | PHAST | software resource | A freely available software package for comparative and evolutionary genomics that consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations. For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. It consists of over 60,000 lines of C code. | evolutionary genomic, evolution, genomics, sequence alignment, phylogenetic tree, genomic annotation, functional element, protein-coding exon, conserved sequence, phylogenetic modeling, ancestral sequence, c |
is listed by: OMICtools is listed by: Debian has parent organization: Cornell University; New York; USA |
NIH ; David and Lucile Packard Foundation ; NHGRI ; University of California Biotechnology Research and Education Program ; NSF DBI-0644111; NIGMS R01-GM082901-01 |
PMID:21278375 DOI:10.1093/bib/bbq072 |
Free, Available for download, Freely available | OMICS_01557 | https://sources.debian.org/src/phast/ | SCR_003204 | Phylogenetic Analysis with Space/Time Models | 2026-02-14 02:00:42 | 58 | ||||
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Ensembl Resource Report Resource Website 10000+ mentions |
Ensembl (RRID:SCR_002344) | data or information resource, database | Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species. | collection, genome, dataset, database, vertebrate, eukaryotic, DNA, protein, sequence, search, automaticly, annotate, data, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: Animal QTLdb is used by: ChannelPedia is used by: Blueprint Epigenome is used by: HmtPhenome lists: Ensembl Covid-19 is listed by: OMICtools is listed by: Biositemaps is listed by: re3data.org is listed by: LabWorm is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Ensembl Genomes is related to: GermOnline is related to: CandiSNPer is related to: Human Splicing Finder is related to: NGS-SNP is related to: Sanger Mouse Resources Portal is related to: DECIPHER is related to: Ensembl Genomes is related to: PeptideAtlas is related to: AnimalTFDB is related to: Bgee: dataBase for Gene Expression Evolution is related to: FlyMine is related to: Rat Gene Symbol Tracker is related to: UniParc at the EBI is related to: go-db-perl is related to: UniParc is related to: g:Profiler is related to: RIKEN integrated database of mammals is related to: VBASE2 is related to: p300db is related to: ShinyGO has parent organization: European Bioinformatics Institute has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is parent organization of: Ensembl Metazoa is parent organization of: Ensembl Variation is parent organization of: Pre Ensembl is parent organization of: Variant Effect Predictor is parent organization of: Ensembl Bacteria is parent organization of: Ensembl Plants is parent organization of: Ensembl Fungi is parent organization of: Ensembl Protists is parent organization of: Ensembl Genome Browser works with: Genotate works with: CellPhoneDB works with: Open Regulatory Annotation Database works with: Database of genes related to Repeat Expansion Diseases works with: TarBase |
Wellcome Trust ; EMBL ; European Union ; FP7 ; FP6 ; MRC ; NHGRI ; BBSRC |
PMID:24316576 PMID:23203987 |
nif-0000-21145, OMICS_01647, biotools:ensembl, r3d100010228 | https://bio.tools/ensembl https://sources.debian.org/src/ensembl/ https://doi.org/10.17616/R39K5B |
SCR_002344 | ENSEMBL | 2026-02-14 02:00:23 | 11652 | ||||||
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JBrowse Resource Report Resource Website 10+ mentions |
JBrowse (RRID:SCR_001004) | JBrowse | software resource | A high-performance visualization tool for interactive exploration of large, integrated genomic datasets written primarily in JavaScript. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations. | genome |
is used by: Genome Resources for Yeast Chromosomes is listed by: OMICtools is listed by: Debian has parent organization: Broad Institute |
NHGRI 5R01HG004483-09 | PMID:22517427 PMID:21221095 |
GNU Lesser General Public License, Account required | OMICS_00918 | https://sources.debian.org/src/jbrowse/ | SCR_001004 | 2026-02-14 01:59:53 | 32 | |||||
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MGED Ontology Resource Report Resource Website 1+ mentions |
MGED Ontology (RRID:SCR_004484) | MO | data or information resource, ontology, controlled vocabulary | An ontology including concepts, definitions, terms, and resources for a standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1. These terms will enable structure queries of elements of the experiments. Furthermore, the terms will also enable unambiguous descriptions of how the experiment was performed. | microarray, biomaterial, treatment, mage, owl |
is listed by: BioPortal is related to: MIAME is related to: MIAME is related to: RNA Abundance Database has parent organization: Functional Genomics Data Society has parent organization: SourceForge |
NIBIB ; NHGRI P41HG003619 |
PMID:16428806 | nlx_47223 | http://purl.bioontology.org/ontology/MO | SCR_004484 | Microarray and Gene Expression Data Ontology | 2026-02-14 02:00:59 | 1 | |||||
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SO Resource Report Resource Website 10+ mentions |
SO (RRID:SCR_004374) | SO | data or information resource, ontology, controlled vocabulary | A collaborative ontology for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. The OBO revision is available here: http://sourceforge.net/p/song/svn/HEAD/tree/ SO includes different kinds of features which can be located on the sequence. Biological features are those which are defined by their disposition to be involved in a biological process. Biomaterial features are those which are intended for use in an experiment such as aptamer and PCR_product. There are also experimental features which are the result of an experiment. SO also provides a rich set of attributes to describe these features such as polycistronic and maternally imprinted. The Sequence Ontologies use the OBO flat file format specification version 1.2, developed by the Gene Ontology Consortium. The ontology is also available in OWL from Open Biomedical Ontologies. This is updated nightly and may be slightly out of sync with the current obo file. An OWL version of the ontology is also available. The resolvable URI for the current version of SO is http://purl.obolibrary.org/obo/so.owl. | annotation, sequence, biological sequence, sequence variation, genome, genome annotation, owl, FASEB list |
is listed by: BioPortal is related to: ASOoViR is related to: VAGrENT has parent organization: OBO has parent organization: Gene Ontology |
NHGRI HG02273 | PMID:20796305 PMID:20226267 PMID:18629179 PMID:15892872 |
The community can contribute to this resource | nlx_38918 | SCR_004374 | Sequence Ontology Project, Sequence Types and Features Ontology, Sequence Ontology | 2026-02-14 02:00:58 | 44 | |||||
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OligoGenome Resource Report Resource Website 1+ mentions |
OligoGenome (RRID:SCR_006025) | OligoGenome | data or information resource, database, resource | The Stanford Human OligoGenome Project hosts a database of capture oligonucleotides for conducting high-throughput targeted resequencing of the human genome. This set of capture oligonucleotides covers over 92% of the human genome for build 37 / hg19 and over 99% of the coding regions defined by the Consensus Coding Sequence (CCDS). The capture reaction uses a highly multiplexed approach for selectively circularizing and capturing multiple genomic regions using the in-solution method developed in Natsoulis et al, PLoS One 2011. Combined pools of capture oligonucleotides selectively circularize the genomic DNA target, followed by specific PCR amplification of regions of interest using a universal primer pair common to all of the capture oligonucleotides. Unlike multiplexed PCR methods, selective genomic circularization is capable of efficiently amplifying hundreds of genomic regions simultaneously in multiplex without requiring extensive PCR optimization or producing unwanted side reaction products. Benefits of the selective genomic circularization method are the relative robustness of the technique and low costs of synthesizing standard capture oligonucleotide for selecting genomic targets. | oligonucleotide, genome, probe, coding region, oligonucleotide sequence, chromosome | has parent organization: Stanford University; Stanford; California | NHGRI RC2 HG005570-01; NCI R21CA12848; NCI 5K08CA96879?6; NIDDK DK56339; NHGRI 2P01HG000205; NLM T15-LM007033; Doris Duke Clinical Foundation ; Reddere Foundation ; Liu Bie Ju Cha and Family Fellowship in Cancer ; Wang Family Foundation ; Howard Hughes Medical Foundation |
PMID:22102592 | nlx_151422 | SCR_006025 | Stanford Human Oligo Genome Project, Human OligoGenome Resource, Stanford Human Oligo Genome, Human Oligo Genome, Human OligoGenome | 2026-02-14 02:01:13 | 2 | ||||||
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ASprofile Resource Report Resource Website 10+ mentions |
ASprofile (RRID:SCR_001833) | ASprofile | software resource | A suite of programs for extracting, quantifying and comparing alternative splicing (AS) events from RNA-seq data. | alternative splicing event, rna-seq, alternative splicing |
is listed by: OMICtools has parent organization: Johns Hopkins University; Maryland; USA |
NHGRI R01-HG006677 | PMID:24555089 | Free, Available for download, Freely available | OMICS_01942 | SCR_001833 | 2026-02-14 02:00:08 | 37 | ||||||
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Consed Resource Report Resource Website 500+ mentions |
Consed (RRID:SCR_005650) | Consed | software resource | A graphical tool for sequence finishing (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence) | next-generation sequencing, graphical editor, linux, macosx, solaris, c++ |
is listed by: OMICtools has parent organization: University of Washington; Seattle; USA |
NIH ; NHGRI R01HG005710 |
PMID:23995391 PMID:9521923 |
Free for academic use, Free for non-profit use, Commercial license | OMICS_00879 | SCR_005650 | 2026-02-14 02:01:08 | 595 | ||||||
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Adult Mouse Anatomy Ontology Resource Report Resource Website 1+ mentions |
Adult Mouse Anatomy Ontology (RRID:SCR_006568) | MA | data or information resource, ontology, controlled vocabulary |
Ontology that organizes anatomical structures for the adult mouse (Theiler stage 28) spatially and functionally, using ''is a'' and ''part of'' relationships. The ontology is used to describe expression data for the adult mouse and phenotype data pertinent to anatomy in standardized ways. The browser can be used to view anatomical terms and their relationships in a hierarchical display. |
functionally, adult mouse, anatomical, anatomy, phenotype, postnatal, structure, theiler stage 28, obo, gene expression |
is listed by: BioPortal is related to: Bgee: dataBase for Gene Expression Evolution has parent organization: Gene Expression Database |
NIH ; NICHD HD33745; NICHD F32 HD08435-01; NHGRI F32 HG00215-01 |
Acknowledgement requested | nif-0000-10300 | http://purl.bioontology.org/ontology/MA | SCR_006568 | Adult Mouse Anatomy Browser, MGI Adult Mouse Anatomical Dictionary Browser, Adult Mouse Anatomical Dictionary Browser, Mouse Adult Gross Anatomy Ontology, Anatomical Dictionary for the Adult Mouse | 2026-02-14 02:01:19 | 3 | |||||
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Consensus Measures for Phenotype and Exposure Resource Report Resource Website 1+ mentions |
Consensus Measures for Phenotype and Exposure (RRID:SCR_006688) | PhenX | knowledge environment | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on 05 01 2025. PhenX is a project to prioritize Phenotype and eXposure measures for Genome-wide Association Studies (GWAS). Leaders of the scientific community will assess and prioritize a broad range of domains relevant to genomics research and public health. The PhenX Steering Committee (SC), chaired by Dr. Jonathan Haines, provides leadership in the selection of domains and domain experts. Members of the SC include outstanding scientists from the research community and liaisons from the Institutes and Centers of the National Institutes of Health. Consensus measures for GWAS will have a direct impact on biomedical research and ultimately on public health. During the course of this project, up to 20 research domains will be examined, with up to 15 measures being recommended for use in future GWAS and other large-scale genomic research efforts. The goal is to maximize the benefits of future research by having comparable measures so that studies can be integrated. Each selected domain will be reviewed by a Working Group (WG) of scientists who are experts in the research area. A systematic review of the literature will guide the WGs selection of up to 15 high priority measures with standardized approaches for measurement. Selection criteria for the measures include factors such as validity, reproducibility, cost, feasibility, and burden to both investigators and participants. The scientific community will be asked to provide input on proposed measures. Consensus development is a key component of the project. | biomedical, domain, genome, health, phenotype, public, research |
has parent organization: RTI International is parent organization of: Phenotypes and eXposures Toolkit is parent organization of: PhenX Phenotypic Terms has organization facet: Phenotypes and eXposures Toolkit |
NHGRI U01 HG004597 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-32816 | SCR_006688 | PhenX - consensus measures for Phenotypes and eXposures, Consensus Measures for Phenotypes Exposures, PhenX (consensus measures for Phenotypes and eXposures), Consensus Measures for Phenotypes Exposure, Consensus Measures for Phenotypes and Exposures | 2026-02-14 02:01:22 | 1 | ||||||
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Resource Discovery System Resource Report Resource Website |
Resource Discovery System (RRID:SCR_005554) | RDS | data or information resource, database | Resource Discovery System is a web-accessible and searchable inventory of biomedical research resources. Powered by the Resource Discovery System (RDS) that includes a standards-based informatics infrastructure * Biositemaps Information Model * Biomedical Resource Ontology Extensions * Web Services distributed web-accessible inventory framework * Biositemap Resource Editor * Resource Discovery System Source code and project documentation to be made available on an open-source basis. Contributing institutions: University of Pittsburgh, University of Michigan, Stanford University, Oregon Health & Science University, University of Texas Houston. Duke University, Emory University, University of California Davis, University of California San Diego, National Institutes of Health, Inventory Resources Working Group Members | registry, web service, source code, biomedical, software resource, material resource, funding resource, service resource, training resource, people resource | has parent organization: Biositemaps | Clinical and Translational Science Awards Consortium ; National Centers for Biomedical Computing ; NCRR 3UL1RR024153-03S1; NCRR 5UL1RR024128-03S1; NCRR 1UL1RR025008-01; NCRR 1UL1RR024146-01; NCRR 1UL1RR024986-01; NCRR 1UL1RR024153-01; NIDA 3U54DA021519-04S1; NHGRI 3U54HG004028-04S |
nlx_144645 | SCR_005554 | 2026-02-14 02:06:28 | 0 | ||||||||
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MethylomeDB Resource Report Resource Website 1+ mentions |
MethylomeDB (RRID:SCR_005583) | MethylomeDB | data or information resource, database | A database containing genome-wide brain DNA methylation profiles for human and mouse brains. The DNA methylation profiles were generated by Methylation Mapping Analysis by Paired-end Sequencing (Methyl-MAPS) method and analyzed by Methyl-Analyzer software package. The methylation profiles cover over 80% CpG dinucleotides in human and mouse brains in single-CpG resolution. The integrated genome browser (modified from UCSC Genome Browser allows users to browse DNA methylation profiles in specific genomic loci, to search specific methylation patterns, and to compare methylation patterns between individual samples. Two species were included in the Brain Methylome Database: human and mouse. Human postmortem brain samples were obtained from three distinct cortical regions, i.e., dorsal lateral prefrontal cortex (dlPFC), ventral prefrontal cortex (vPFC), and auditory cortex (AC). Human samples were selected from our postmortem brain collection with extensive neuropathological and psychopathological data, as well as brain toxicology reports. The Department of Psychiatry of Columbia University and the New York State Psychiatric Institute have assembled this brain collection, where a validated psychological autopsy method is used to generate Axis I and II DSM IV diagnoses and data are obtained on developmental history, history of psychiatric illness and treatment, and family history for each subject. The mouse sample (strain 129S6/SvEv) DNA was collected from the entire left cerebral hemisphere. The three human brain regions were selected because they have been implicated in the neuropathology of depression and schizophrenia. Within each cortical region, both disease and non-psychiatric samples have been profiled (matching subjects by age and sex in each group). Such careful matching of subjects allows one to perform a wide range of queries with the ability to characterize methylation features in non-psychiatric controls, as well as detect differentially methylated domains or features between disease and non-psychiatric samples. A total of 14 non-psychiatric, 9 schizophrenic, and 6 depression methylation profiles are included in the database. | brain, dna methylation, dorsal lateral prefrontal cortex, ventral prefrontal cortex, auditory cortex, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Columbia University; New York; USA |
NIH ; NHGRI HG002915; NIMH MH074118 |
PMID:22140101 | OMICS_01843, nlx_146210, biotools:methylomedb | https://bio.tools/methylomedb | SCR_005583 | MethylomeDB - the Brain Methylome Database, Brain Methylome Database | 2026-02-14 02:06:24 | 1 | |||||
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Transcriptional Regulatory Element Database Resource Report Resource Website 50+ mentions |
Transcriptional Regulatory Element Database (RRID:SCR_005661) | TRED | data or information resource, database | Collects mammalian cis- and trans-regulatory elements together with experimental evidence. Regulatory elements were mapped on to assembled genomes. Resource for gene regulation and function studies. Users can retrieve primers, search TF target genes, retrieve TF motifs, search Gene Regulatory Networks and orthologs, and make use of sequence analysis tools. Uses databases such as Genbank, EPD and DBTSS, and employ promoter finding program FirstEF combined with mRNA/EST information and cross-species comparisons. Manually curated. | Mammalian, cis, trans, regulatory, element, mapped, genome, gene, regulation, function, data, FASEB list |
uses: GenBank uses: Eukaryotic Promoter Database uses: DBTSS: Database of Transcriptional Start Sites has parent organization: Cold Spring Harbor Laboratory |
NCI ; NHGRI HG001696 |
PMID:17202159 | Free, Freely available | nif-0000-03585 | SCR_005661 | Transcriptional Regulatory Element Database | 2026-02-14 02:05:57 | 78 |
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