Searching the RRID Resource Information Network

Our searching services are busy right now. Please try again later

  • Register
X
Forgot Password

If you have forgotten your password you can enter your email here and get a temporary password sent to your email.

X

Leaving Community

Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.

No
Yes

Preparing word cloud

×

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.

Search

Type in a keyword to search

Filter by records added date
See new records

Options


Current Facets and Filters

  • Keywords:gene (facet)

Facets


Recent searches

Snippet view Table view
Click the to add this resource to a Collection

1,737 Results - per page

Show More Columns | Download Top 1000 Results

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
GAGE
 
Resource Report
Resource Website
50+ mentions
GAGE (RRID:SCR_017067) data processing software, software application, software resource, data analysis software Software R package for gene set enrichment or pathway analysis. Applicable independent of microarray or RNAseq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. Pipeline routines of multiple GAGE analyses in batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources and studies. gene, set, enrichment, pathway, batch, comparison, parallel, analysis, heterogeneous, data is listed by: Bioconductor
is related to: R Project for Statistical Computing
Free, Available for download, Freely available SCR_017067 Generally Applicable Gene-set Enrichment for pathway analysis, gage, Generally Applicable Gene-set Enrichment, GSEA 2026-08-04 09:44:04 50
RNAmmer
 
Resource Report
Resource Website
100+ mentions
RNAmmer (RRID:SCR_017075) data analysis service, data processing software, data analysis software, analysis service resource, web service, standalone software, software resource, software application, data access protocol, production service resource, service resource Software package to predict ribosomal RNA genes in full genome sequences by utilising two levels of Hidden Markov Models. Consistent and rapid annotation of ribosomal RNA genes. predict, ribosomal, RNA, gene, full, genome, sequence, HMM, rRNA has parent organization: Technical University of Denmark; Lyngby; Denmark EMBIO at the University of Oslo ;
Research Council of Norway ;
Danish Center for Scientific Computing ;
European Union
PMID:17452365 Restricted SCR_017075 2026-08-04 09:44:04 103
Arabidopsis Gene Regulatory Information Server
 
Resource Report
Resource Website
10+ mentions
Arabidopsis Gene Regulatory Information Server (RRID:SCR_006928) AGRIS database, data or information resource An information resource of Arabidopsis promoter sequences, transcription factors and their target genes that contains three databases. *AtcisDB consists of approximately 33,000 upstream regions of annotated Arabidopsis genes (TAIR9 release) with a description of experimentally validated and predicted cis-regulatory elements. *AtTFDB contains information on approximately 1,770 transcription factors (TFs). These TFs are grouped into 50 families, based on the presence of conserved domains. *AtRegNet contains 11,355 direct interactions between TFs and target genes. They provide free download of Arabidopsis thaliana cis-regulatory database (AtcisDB) and transcription factor database (AtTFDB). gene regulatory, gene, arabidopsis thaliana, promoter sequence, target gene, transcription factor, FASEB list is listed by: OMICtools
has parent organization: Ohio State University; Ohio; USA
NSF PMID:21059685
PMID:16524982
PMID:12820902
Free, Acknowledgement requested OMICS_00548, nif-0000-02540 SCR_006928 2026-08-04 09:41:43 49
EMBRYS
 
Resource Report
Resource Website
1+ mentions
EMBRYS (RRID:SCR_006689) EMBRYS database, data or information resource Data collection of gene expression patterns mapped in whole-mount mouse embryo (ICR strain) of mid-gestational stages (Embryonic Day 9.5, 10.5, 11.5), in which most striking dynamics in pattern formation and organogenesis is observed. Collection of gene expression patterns of transcription factors (TFs) and TF-related factors such as transcription cofactors. Genes were extracted from databases including RIKEN Transcription Factor Database and Panther Classification System. Gene, expression, pattern, mapped, whole mount, mouse, embryo, ICR strain, mid gestational stage, transcription, factor, cofactor, data uses: RIKEN
uses: MGC
uses: PANTHER
Japanese Ministry of Education Culture Sports Science and Technology MEXT ;
Japanese Ministry of Health Labor and Welfare
Free, Freely available nlx_153839 http://embrys.jp/embrys/html/MainMenu.html SCR_006689 Embryonic Gene Expression Database for Biomedical Research Source, Embryonic gene expression Database as a Biomedical Research Source 2026-08-04 09:41:40 8
UniSTS
 
Resource Report
Resource Website
10+ mentions
UniSTS (RRID:SCR_006843) UniSTS database, data or information resource THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences. Chromosome maps are labeled by name of the originating organism, the map title, total markers, total UniSTSs and links to view maps as well as research documents available through PubMed, another NCBI database. The search functions within UniSTS allow the user to search by gene marker, chromosome, gene symbol and gene description terms to locate markers on specified genes. A representation of the UniSTS datasets is available by ftp. NOTE: All data from this resource have been moved to the Probe database, http://www.ncbi.nlm.nih.gov/probe. You can retrieve all UniSTS records by searching the probe database using the search term unists(properties). (use brackets insead of parenthesis). Additionally, legacy data remain on the NCBI FTP Site in the UniSTS Repository (ftp://ftp.ncbi.nih.gov/pub/ProbeDB/legacy_unists). marker, primer sequence, mapping, sequence tagged site, genomic position, gene, sequence, nucleotide, nucleotide sequence, chromosome, gold standard is listed by: re3data.org
is related to: NCBI Probe
has parent organization: NCBI
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-03614 SCR_006843 UniSTS: Integrating Markers and Maps, NCBI UniSTS, Entrez UniSTS 2026-08-04 09:41:42 40
AthaMap
 
Resource Report
Resource Website
10+ mentions
AthaMap (RRID:SCR_006717) database, data or information resource Genome wide map of putative transcription factor binding sites in Arabidopsis thaliana genome.Data in AthaMap is based on published transcription factor (TF) binding specificities available as alignment matrices or experimentally determined single binding sites.Integrated transcriptional and post transcriptional data.Provides web tools for analysis and identification of co-regulated genes. Provides web tools for database assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana. gene, arabidopsis thaliana, binding site, genome, transcription factor, small rna binding site, small rna, rna, microrna, cis-regulatory element, post-transcriptional regulation, FASEB list is listed by: OMICtools
is listed by: bio.tools
has parent organization: Technical University of Braunschweig; Braunschweig; Germany
PMID:22800758
PMID:21177332
PMID:18842622
PMID:17148485
PMID:16922688
PMID:15980498
PMID:14681436
Free, Freely available nif-0000-02583, biotools:athamap, OMICS_00549, nif-0000-20814, SCR_013106 https://bio.tools/athamap SCR_006717 Arabidopsis thaliana Map 2026-08-04 09:41:41 48
Biomolecular Object Network Databank
 
Resource Report
Resource Website
10+ mentions
Biomolecular Object Network Databank (RRID:SCR_007433) database, data or information resource 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 on August 19,2019.BOND, which requires registration of a free account, is a resource used to perform cross-database searches of available sequence, interaction, complex and pathway information. BOND integrates a range of component databases including GenBank and BIND, the Biomolecular Interaction Network Database. BOND contains 70+ million biological sequences, 33,000 structures, 38,000 GO terms, and over 200,000 human curated interactions contained in BIND, and is open access. BOND serves the interests of the developing global interactome effort encompassing the genomic, proteomic and metabolomic research communities. BOND is the first open access search resource to integrate sequence and interaction information. BOND integrates BLAST functionality, and contains a well-documented API. BOND also stores annotation links for sequences, including links to Genome Ontology descriptions, MedLine abstracts, taxon identifiers, associated structures, redundant sequences, sequence neighbors, conserved domains, data base cross-references, Online Mendalian Inheritance in Man identifiers, LocusLink identifiers and complete genomes. BIND on BOND The Biomolecular Interaction Network Database (BIND), a component database of BOND, is a collection of records documenting molecular interactions. The contents of BIND include high-throughput data submissions and hand-curated information gathered from the scientific literature. BIND is an interaction database with three classifications for molecular associations: molecules that associate with each other to form interactions, molecular complexes that are formed from one or more interaction(s) and pathways that are defined by a specific sequence of two or more interactions.Interactions A BIND record represents an interaction between two or more objects that is believed to occur in a living organism. A biological object can be a protein, DNA, RNA, ligand, molecular complex, gene, photon or an unclassified biological entity. BIND records are created for interactions which have been shown experimentally and published in at least one peer-reviewed journal. A record also references any papers with experimental evidence that support or dispute the associated interaction. Interactions are the basic units of BIND and can be linked together to form molecular complexes or pathways. The BIND interaction viewer is a tool to visualize and analyze molecular interactions, complexes and pathways. The BIND interaction viewer uses Ontoglyphs to display information about a protein via attributes such as molecular function, biological process and sub-cellular localization. Ontoglyphs allow to graphically and interactively explore interaction networks, by visualizing interactions in the context of 34 functional, 25 binding specificity and 24 sub-cellular localization Ontoglyphs categories. We will continue to provide an open access version of BOND, providing its subscribers with free, unlimited access to a core content set. But we are confident you will soon want to upgrade to BONDplus. gene, genes, genome, annotation, binding specificity, biological process, complex, dna, genomes, genomic, human, interaction, interactome, ligand, metabolomic, molecular, molecular complex, molecular function, molecular interaction, mouse, ontoglyphs, ontology terms, pathway, photon, protein, protein-protein interactions, proteomic, rna, sequence, structure, sub-cellular localization, taxonomy, unclassified biological entity THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-00571 SCR_007433 BOND 2026-08-04 09:41:52 17
National Cell Repository for Alzheimer's Disease
 
Resource Report
Resource Website
10+ mentions
National Cell Repository for Alzheimer's Disease (RRID:SCR_007313) NCRAD biomaterial supply resource, material resource, tissue bank Cell repository for Alzheimer's disease that collects and maintains biological specimens and associated data. Its data is derived from large numbers of genetically informative, phenotypically well-characterized families with multiple individuals affected with Alzheimer's disease, as well as individuals for case-control studies. gene, alzheimers disease, dementia, dna, late onset, memory loss, phenotypic data, research study, clinical data, plasma, serum, rna, brain tissue, family history, blood is listed by: One Mind Biospecimen Bank Listing
is related to: DIAN - Dominantly Inherited Alzheimer Network
is related to: Alzheimers Disease Genetics Consortium
is related to: National Alzheimer's Coordinating Center
has parent organization: Indiana University; Indiana; USA
Alzheimer's disease, Late-onset Alzheimer's disease, Dementia, Memory loss NIA ;
NIH Blueprint for Neuroscience Research
Public, Application required for genetic research nif-0000-00178 SCR_007313 2026-08-04 09:41:49 35
5S Ribosomal RNA Database
 
Resource Report
Resource Website
1+ mentions
5S Ribosomal RNA Database (RRID:SCR_007545) 5S Ribosomal RNA Database database, data or information resource A database on nucleotide sequences of 5S rRNAs and their genes. The database contains 1985 primary structures of 5S rRNA and 5S rDNA, and was last updated in 2002, according to the website. They include 60 archaebacterial, 470 eubacterial, 63 plastid, nine mitochondrial and 1383 eukaryotic sequences. The nucleotide sequences of the 5S rRNAs or 5S rDNAs are divided according to the taxonomic position of the source organisms. The sequences for particular organisms can be retrieved as single files using a taxonomic browser or in multiple sequence structural alignments. The multiple sequence alignments of 5S ribosomal RNAs can be downloaded in TAB-delimited and FASTA formats. eubacteria, eukaryote, archaebacteria, mitochondrion, model rna molecule, nucleotide sequence database, ribosome, plastid, ribosomal rna, sequence alignment, rna-protein interaction, rna, rna structure, 5s rrna, gene, 5s rdna, mitochondria, sequence, alignment has parent organization: Polish Academy of Sciences Warsaw; Warsaw; Poland Deutsche Agentur fur Raumfahrtangelegenheiten GmbH ;
Fonds der Chemischen Industrie e.V. ;
Polish State Committee for Scientific Research ;
DFG
PMID:10592212 nif-0000-02526 http://rose.man/poznan. pl/5SData/index.html SCR_007545 2026-08-04 09:41:54 6
Allen Mouse Spinal Cord Atlas
 
Resource Report
Resource Website
10+ mentions
Allen Mouse Spinal Cord Atlas (RRID:SCR_007418) Mouse Spinal Cord Atlas atlas, database, data or information resource Platform for exploring spinal cord at cellular and molecular levels. Map of gene expression for adult and juvenile mouse spinal cord. Provides map of normal mouse when used to compare gene expression in diseased or injury models. Interactive database of gene expression mapped across all anatomic segments of mouse spinal cord at postnatal days 4 and 56. Indexed set of images based on RNA in situ hybridization data, searchable and sortable by gene, age, expression, cervical, thoracic, lumbar, sacral, and coccygeal segments. gene, expression, adult, diseased, injury, juvenile, models, mouse, postnatal, RNA, hybridization, spinal, cord, molecular, neuroanatomy, data has parent organization: Allen Institute for Brain Science
has parent organization: Allen Brain Atlas
Free, Freely available nif-0000-00510 http://mousespinal.brain-map.org/ SCR_007418 2026-08-04 09:41:52 29
SysZNF - C2H2 Zinc Finger genes
 
Resource Report
Resource Website
SysZNF - C2H2 Zinc Finger genes (RRID:SCR_007056) SysZNF database, data or information resource THIS RESOURCE IS NO LONGER IN SERVICE, documented September 2, 2016. SysZNF is an information resource for C2H2 Zinc Finger genes in humans and mice. C2H2 Zinc Finger genes (C2H2-ZNF) constitute the largest class of transcription factors in humans and mouse. C2H2 zinc finger proteins primarily bind to DNA. In most cases, they attach to regions near certain genes and turn the genes on and off as needed. The researches on these genes show light on the evolution of gene regulation systems and development. Therefore, we develop SysZNF (Systematical information resource of Zinc Finger genes) to collect the information related to C2H2 Zinc Finger genes. The aim of SysZNF was to provide a user-friendly interface for rendering the information (DNA, Expression, Protein, Reference and so on) of each C2H2-ZNF (e.g., ZNF10) and to enable a comprehensive analysis of C2H2-ZNF. This project was supported by the Proteome-Center at Rostock University (PCRU) who conceives the concept of the database and Key laboratory of Systems biology at the Shanghai Institute for Biological Sciences (SIBS) who implemented the database. It is maintained jointly by PCRU and SIBS. zinc finger protein, zinc finger, cysteine, histidine, zinc ion, gene has parent organization: University of Rostock; Mecklenburg-Vorpommern; Germany
has parent organization: Chinese Academy of Sciences; Beijing; China
BMBF 2007DFA31040;
Chinese Academy of Sciences CHN07/38
PMID:18974185 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-03530 SCR_007056 SysZNF: the C2H2 Zinc Finger Gene Database, SysZNF: the Zinc Finger gene database 2026-08-04 09:41:45 0
MIPS Ustilago maydis Database
 
Resource Report
Resource Website
1+ mentions
MIPS Ustilago maydis Database (RRID:SCR_007563) database, data or information resource The MIPS Ustilago maydis Genome Database aims to present information on the molecular structure and functional network of the entirely sequenced, filamentous fungus Ustilago maydis. The underlying sequence is the initial release of the high quality draft sequence of the Broad Institute. The goal of the MIPS database is to provide a comprehensive genome database in the Genome Research Environment in parallel with other fungal genomes to enable in depth fungal comparative analysis. The specific aims are to: 1. Generate and assemble Whole Genome Shotgun sequence reads yielding 10X coverage of the U. maydis genome 2. Integrate the genomic sequence assembly with physical maps generated by Bayer CropScience 3. Perform automated annotation of the sequence assembly 4. Align the strain 521 assembly with the FB1 assembly provided by Exelixis 5. Release the sequence assembly and results of our annotation and analysis to public Ustilago maydis is a basidiomycete fungal pathogen of maize and teosinte. The genome size is approximately 20 Mb. The fungus induces tumors on host plants and forms masses of diploid teliospores. These spores germinate and form haploid meiotic products that can be propagated in culture as yeast-like cells. Haploid strains of opposite mating type fuse and form a filamentous, dikaryotic cell type that invades plant tissue to reinitiate infection. Ustilago maydis is an important model system for studying pathogen-host interactions and has been studied for more than 100 years by plant pathologists. Molecular genetic research with U. maydis focuses on recombination, the role of mating in pathogenesis, and signaling pathways that influence virulence. Recently, the fungus has emerged as an excellent experimental model for the molecular genetic analysis of phytopathogenesis, particularly in the characterization of infection-specific morphogenesis in response to signals from host plants. Ustilago maydis also serves as an important model for other basidiomycete plant pathogens that are more difficult to work with in the laboratory, such as the rust and bunt fungi. Genomic sequence of U. maydis will also be valuable for comparative analysis of other fungal genomes, especially with respect to understanding the host range of fungal phytopathogens. The analysis of U. maydis would provide a framework for studying the hundreds of other Ustilago species that attack important crops, such as barley, wheat, sorghum, and sugarcane. Comparisons would also be possible with other basidiomycete fungi, such as the important human pathogen C. neoformans. Commercially, U. maydis is an excellent model for the discovery of antifungal drugs. In addition, maize tumors caused by U. maydis are prized in Hispanic cuisine and there is interest in improving commercial production. The complete putative gene set of the Broad Institute''s second release is loaded into the database and in addition all deviating putative genes from a putative gene set produced by MIPS with different gene prediction parameters are also loaded. The complete dataset will then be analysed, gene predictions will be manually corrected due to combined information derived from different gene prediction algorithms and, more important, protein and EST comparisons. Gene prediction will be restricted to ORFs larger than 50 codons; smaller ORFs will be included only if similarities to other proteins or EST matches confirm their existence or if a coding region was postulated by all prediction programs used. The resulting proteins will be annotated. They will be classified according to the MIPS classification catalogue receiving appropriate descriptions. All proteins with a known, characterized homolog will be automatically assigned to functional categories using the MIPS functional catalog. All extracted proteins are in addition automatically analysed and annotated by the PEDANT suite. drug, environment, filamentous, functional, fungal, fungal genome databases, fungus, gene, genetic, basidiomycete, cell, codon, culture, dikaryotic, diploid, genome, genomic, germinate, haploid, host, human, infection, maize, mating, meiotic, model, molecular, morphogenesis, network, orf, pathogen, pathologist, phytopathogen, phytopathogenesis, plant, protein, recombination, sequence, signal, spore, strain, structure, teliospore, teosinte, tissue, tumor, ustilago maydis, virulence, yeast nif-0000-21276 SCR_007563 MUMDB 2026-08-04 09:41:55 9
POOLSCORE
 
Resource Report
Resource Website
POOLSCORE (RRID:SCR_007514) software application, software resource Software program for analysis of case-control genetic association studies using allele frequency measurements on DNA pools (entry from Genetic Analysis Software) gene, genetic, genomic, r is listed by: Genetic Analysis Software SCR_009373, nlx_154595, nlx_154087 SCR_007514 R/POOLSCORE 2026-08-04 09:41:52 0
Atlas of Genetics and Cytogenetics in Oncology and Haematology
 
Resource Report
Resource Website
10+ mentions
Atlas of Genetics and Cytogenetics in Oncology and Haematology (RRID:SCR_007199) atlas, database, data or information resource Online journal and database devoted to genes, cytogenetics, and clinical entities in cancer, and cancer-prone diseases. Its aim is to cover the entire field under study and it presents concise and updated reviews (cards) or longer texts (deep insights) concerning topics in cancer research and genomics. gene, cytogenetic, cancer, cancer research, genomic, online journal, bio.tools, FASEB list is listed by: Debian
is listed by: bio.tools
PMID:23161685 Freely available, Available to the scientific community nif-0000-30129, biotools:atlasgeneticsoncology https://bio.tools/atlasgeneticsoncology SCR_007199 Genetics and Cytogenetics Atlas 2026-08-04 09:41:46 38
GOA
 
Resource Report
Resource Website
500+ mentions
GOA (RRID:SCR_007691) GOA, GOA REF database, data or information resource An annotation program which aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). It is a central dataset for other major multi-species databases, such as Ensembl and NCBI. Because of the multi-species nature of the UniProtKB, UniProtKB-GOA assists in the curation of 200,000 species. This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups. Gene Association Files can be accessed from the Downloads section of the website. gene ontology, chicken proteome, cow proteome, human proteome, xref, gene, gene association, gold standard is listed by: GUDMAP Ontology
is listed by: NIDDK Information Network (dkNET)
is related to: FlyMine
is related to: UniProt DAS
is related to: IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures
has parent organization: European Bioinformatics Institute
Public, Available to the research community, All UniProtKB-GOA Gene Association Files are released approximately every four weeks nif-0000-02916 SCR_007691 UniProtKB-GOA, Gene Ontology Annotation (UniProtKB-GOA) Database, GOA - Gene Ontology Annotation, Gene Ontology Annotation, GO Annotation at EBI 2026-08-04 09:41:57 570
miRpathDB
 
Resource Report
Resource Website
50+ mentions
miRpathDB (RRID:SCR_017356) web service, software resource, data access protocol, database, data or information resource Collection of single miRNAs that regulate pathways, gene ontologies and other categories, hence complementing available miRNA target enrichment programs, tailored for miRNA sets. New dictionary on microRNAs and target pathways. Database to augment available target pathway web-servers by providing researches access to information which pathways are regulated by miRNA, which miRNAs target pathway and how specific regulations are. Collection, miRNA, data, pathway, gene, ontology, dataset, dictionary, target, regulation, bio.tools is listed by: bio.tools
is listed by: Debian
Saarland University ;
Germany
PMID:27742822 biotools:miRPathDb https://bio.tools/miRPathDB SCR_017356 miRNA Pathway Dictionary Database 2026-08-04 09:44:09 52
SynGO
 
Resource Report
Resource Website
100+ mentions
SynGO (RRID:SCR_017330) data analysis service, analysis service resource, controlled vocabulary, production service resource, service resource, ontology, data or information resource Evidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms. Synapse, evidence, curated, base, reference, analysis, omics, data, ontology, gene, annotation uses: Gene Ontology Stanley Center for Psychiatric Research at The Broad Institute of MIT and Harvard ;
European Union ;
CERCA Program/Generalitat de Catalunya ;
NINDS NS36251;
German Federal Ministry of Education and Research
PMID:31171447 Free, Freely available SCR_017330 Synaptic Gene Ontologies 2026-08-04 09:44:09 134
shinyGEO
 
Resource Report
Resource Website
shinyGEO (RRID:SCR_017605) analysis service resource, software resource, production service resource, service resource, web application Web based tool to download gene expression datasets from GEO in order to perform differential expression and survival analysis for gene of interest. Produces publication ready graphics and generates R code ensuring that all analyses are reproducible. Web based application for analyzing gene expression omnibus datasets. Gene, expression, dataset, GEO, differencial, analysis, gene, graphic, omnibus, data, bio.tools uses: Shiny
is listed by: Debian
is listed by: bio.tools
has parent organization: Eastern Connecticut State University; Connecticut; United States
works with: Gene Expression Omnibus (GEO)
Google Summer of Code PMID:27503226 Free, Available for download, Freely available biotools:shinygeo https://gdancik.github.io/shinyGEO/, https://bio.tools/shinygeo SCR_017605 2026-08-04 09:44:15 0
Single Cell Developmental Database
 
Resource Report
Resource Website
1+ mentions
Single Cell Developmental Database (RRID:SCR_017546) SCDevDB data set, storage service resource, data repository, service resource, database, data or information resource Database for insights into single cell gene expression profiles during human developmental processes. Interactive database provides DE gene lists in each developmental pathway, t-SNE map, and GO and KEGG enrichment analysis based on these differential genes. Single, cell, gene, expression, profile, human, development, process, data RGC General Research Fund ;
GRF Research Project
DOI:10.3389/fgene.2019.00903 Free, Available for download, Freely available SCR_017546 Single-Cell Developmental Database 2026-08-04 09:44:14 2
Transcriptive
 
Resource Report
Resource Website
Transcriptive (RRID:SCR_017545) data processing software, data analysis software, software resource, software application, software toolkit Software tool as bioinformatics analysis pipeline used for RNA sequencing data. Workflow processes raw data from FastQ inputs, aligns reads, generates gene and transcript counts, and performs quality control on results. Analysis, pipeline, RNA, sequencing, data, raw, FastQ, input, align, read, gene, transcript, count, quality, control Free, Available for download, Freely available SCR_017545 2026-08-04 09:44:10 0

Can't find your Tool?

We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.

Can't find the RRID you're searching for? X
X
  1. RRID Portal Resources

    Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.

  2. Navigation

    You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.

  3. Logging in and Registering

    If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.

  4. Searching

    Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:

    1. Use quotes around phrases you want to match exactly
    2. You can manually AND and OR terms to change how we search between words
    3. You can add "-" to terms to make sure no results return with that term in them (ex. Cerebellum -CA1)
    4. You can add "+" to terms to require they be in the data
    5. Using autocomplete specifies which branch of our semantics you with to search and can help refine your search
  5. Collections

    If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.

  6. Facets

    Here are the facets that you can filter the data by.

  7. Further Questions

    If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.