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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.

(last updated: Oct 12, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
STARResource, algorithm resource, standalone software, data processing software, software application, sequence analysis software, data analysis software, software resourceSoftware performing alignment of high-throughput RNA-seq data. STAR is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure.alignment, rna, rna-seq, reference, aligner, algorithm, short read, suffix, array, cluster, stitchSCR_015899(STAR, RRID:SCR_015899)NHGRIPMID:23104886Last checked up
ASprofileResource, software resourceA suite of programs for extracting, quantifying and comparing alternative splicing (AS) events from RNA-seq data.alternative splicing event, rna-seq, alternative splicingSCR_001833(ASprofile, RRID:SCR_001833)Johns Hopkins University; Maryland; USA NHGRIlisted by: OMICtoolsPMID:24555089Last checked upOMICS_01942
PROVEANResource, analysis service resource, software resource, data analysis service, service resource, production service resourceA software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.amino acid substitution, indel, function, protein, amino acid, substitution, protein variant, genome variant, next-generation sequencing, insertion, deletionSCR_002182(PROVEAN, RRID:SCR_002182)J. Craig Venter Institute NHGRI, NIHlisted by: OMICtoolsPMID:23056405Last checked upOMICS_01849
JuicerResource, software resource, software application, data analysis software, data processing softwareSoftware platform for analyzing kilobase resolution Hi-C data. Open source tool for analyzing terabase scale Hi-C datasets. Allowes to transform raw sequence data into normalized contact maps.analysis, kilobase, resolution, Hi-C, data, terabase, dataset, transform, raw, sequence, normalized, contact, mapSCR_017226(Juicer, RRID:SCR_017226)Baylor College of Medicine; Houston; Texas Cancer Prevention Research Institute of Texas, Google Research Award, IBM University Challenge Award, McNair Medical Institute Scholar Award, NHGRI, NHLBI, NIH New Innovator Award, NSF, NVIDIA Research Center Award, PD Soros Fellowship, President Early Career Award in Science and Engineering, Welch FoundationPMID:27467249Last checked up
UBERONResource, ontology, data or information resource, controlled vocabularyAn integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. Uberon consists of over 10000 classes (March 2014) representing structures that are shared across a variety of metazoans. The majority of these classes are chordate specific, and there is large bias towards model organisms and human.anatomy, comparative, evolution, organ system, anatomical structure, body part, organ, tissue, body, vertebrate, function, phenotype, expression, model organism, oboSCR_010668(UBERON, RRID:SCR_010668)OBO ARRA, DOE, NCRR, NHGRI, NSFrelated to: Gene Ontology, used by: Monarch Initiative, Neuroscience Information Framework, listed by: BioPortalPMID:22293552Last checked upnlx_74404
Drosophila anatomy and development ontologiesResource, ontology, data or information resource, controlled vocabularyA structured controlled vocabulary of the anatomy of Drosophila melanogaster. These ontologies are query-able reference sources for information on Drosophila anatomy and developmental stages. They also provide controlled vocabularies for use in annotation and classification of data related to Drosophila anatomy, such as gene expression, phenotype and images. They were originally developed by FlyBase, who continue to maintain them and have used them for over 200,000 annotations of phenotypes and expression. Extensive use of synonyms means that, given a suitably sophisticated autocomplete, users can find relevant content by searching with almost any anatomical term they find in the literature. These ontologies are developed in the web ontology language OWL2. Their extensive formalization in OWL can be used to drive sophisticated query systems.anatomy, development, developmental stage, gene expression, phenotype, owlSCR_001607(Drosophila anatomy and development ontologies, RRID:SCR_001607) SourceForge , FlyBase NHGRIrelated to: OBO, Flannotator, REDfly Regulatory Element Database for Drosophilia, Bgee: a dataBase for Gene Expression EvolutionLast checked downnlx_153871
Distributed Annotation SystemResource, narrative resource, software resource, standard specification, data or information resourceThe Distributed Annotation System (DAS) defines a communication protocol used to exchange annotations on genomic or protein sequences. It is motivated by the idea that such annotations should not be provided by single centralized databases, but should instead be spread over multiple sites. Data distribution, performed by DAS servers, is separated from visualization, which is done by DAS clients. The advantages of this system are that control over the data is retained by data providers, data is freed from the constraints of specific organisations and the normal issues of release cycles, API updates and data duplication are avoided. DAS is a client-server system in which a single client integrates information from multiple servers. It allows a single machine to gather up sequence annotation information from multiple distant web sites, collate the information, and display it to the user in a single view. Little coordination is needed among the various information providers. DAS is heavily used in the genome bioinformatics community. Over the last years we have also seen growing acceptance in the protein sequence and structure communities. A DAS-enabled website or application can aggregate complex and high-volume data from external providers in an efficient manner. For the biologist, this means the ability to plug in the latest data, possibly including a user''s own data. For the application developer, this means protection from data format changes and the ability to add new data with minimal development cost. Here are some examples of DAS-enabled applications or websites for end users: :- Dalliance Experimental Web/Javascript based Genome Viewer :- IGV Integrative Genome Viewer java based browser for many genomes :- Ensembl uses DAS to pull in genomic, gene and protein annotations. It also provides data via DAS. :- Gbrowse is a generic genome browser, and is both a consumer and provider of DAS. :- IGB is a desktop application for viewing genomic data. :- SPICE is an application for projecting protein annotations onto 3D structures. :- Dasty2 is a web-based viewer for protein annotations :- Jalview is a multiple alignment editor. :- PeppeR is a graphical viewer for 3D electron microscopy data. :- DASMI is an integration portal for protein interaction data. :- DASher is a Java-based viewer for protein annotations. :- EpiC presents structure-function summaries for antibody design. :- STRAP is a STRucture-based sequence Alignment Program. Hundreds of DAS servers are currently running worldwide, including those provided by the European Bioinformatics Institute, Ensembl, the Sanger Institute, UCSC, WormBase, FlyBase, TIGR, and UniProt. For a listing of all available DAS sources please visit the DasRegistry. Sponsors: The initial ideas for DAS were developed in conversations with LaDeana Hillier of the Washington University Genome Sequencing Center.annotation, database, software, genomic, protein, sequence, visualization, data, client-server, integration, bioinformatics, genome, structure, data integrationSCR_008427(Distributed Annotation System, RRID:SCR_008427)Uppsala University; Uppsala; Sweden Howard Hughes Medical Institute, NHGRIlisted by: 3DVCLast checked downnif-0000-30177
SOResource, ontology, data or information resource, controlled vocabularyA 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: 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, sequence, biological sequence, sequence variation, genome, genome annotation, owlSCR_004374(SO, RRID:SCR_004374) Gene Ontology , OBO NHGRIrelated to: ASOoViR, VAGrENT, listed by: BioPortalReferences (4)Last checked upnlx_38918
FlyMineResource, data analysis service, data access protocol, production service resource, analysis service resource, database, web service, service resource, software resource, data or information resourceAn integrated database of genomic, expression and protein data for Drosophila, Anopheles, C. elegans and other organisms. You can run flexible queries, export results and analyze lists of data. FlyMine presents data in categories, with each providing information on a particular type of data (for example Gene Expression or Protein Interactions). Template queries, as well as the QueryBuilder itself, allow you to perform searches that span data from more than one category. Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources, to modify existing template queries or to create your own template queries. Access our FlyMine data via our Application Programming Interface (API). We provide client libraries in the following languages: Perl, Python, Ruby and & Java APIanopheles, genome, c. elegans, drosophila, gene, chromosomal location, genomics, proteomics, gene expression, interaction, homology, function, regulation, protein, phenotype, pathway, disease, publicationSCR_002694(FlyMine, RRID:SCR_002694)University of Cambridge; Cambridge; United Kingdom NHGRI, Wellcome Trustrelated to: FlyBase, Universal Protein Resource, Ensembl, InterPro, BioGRID, Research Collaboratory for Structural Bioinformatics Protein Data Bank, Tree families database, IntAct, Gene Ontology, GOA, ArrayExpress, REDfly Regulatory Element Database for Drosophilia, KEGG, ReactomePMID:17615057Last checked upnif-0000-02845
fermiResource, software resource, data processing software, data analysis software, sequence analysis software, software applicationSoftware assembler and analysis tool for whole-genome short-gun sequencing for Illumina reads. Provides tools for error correction, sequence-to-read alignment and comparison between read sets. Used for large genomes.assembler, analysis, whole, genome, short, gun, sequencing, error, correctionSCR_016652(fermi, RRID:SCR_016652)NHGRIlisted by: OMICtoolsPMID:22569178Last checked up
StringTie Resource, software resource, data processing software, data analysis software, sequence analysis software, software applicationSoftware application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ .assembling, RNA, sequence, transcript, gene, alignment, reconstruction, read, analysis, processSCR_016323(StringTie , RRID:SCR_016323)NCI, NHGRI, NIGMS, the Cancer Prevention and Research Institute of TexasPMID:25690850Last checked down
fermi-liteResource, image analysis software, standalone software, data processing software, alignment software, software application, algorithm resource, software resourceStandalone C library as well as a command-line tool for assembling Illumina short reads in small regions. It is an overlap-based assembler used in sequencing to retain heterozygous events and to assemble diploid regions for the purpose of variant calling.assembling, short, read, small, region, sequencing, retain, heterozygous, event, diploid, variant, callingSCR_016112(fermi-lite, RRID:SCR_016112)NHGRI, NIGMSrelated to: IlluminaPMID:26220959Last checked up
Sanger Mouse Resources PortalResource, database, biomaterial supply resource, production service resource, material service resource, service resource, cell repository, material resource, biomaterial manufacture, data or information resourceDatabase of mouse research resources at Sanger: BACs, targeting vectors, targeted ES cells, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen. The Wellcome Trust Sanger Institute generates, characterizes, and uses a variety of reagents for mouse genetics research. It also aims to facilitate the distribution of these resources to the external scientific community. Here, you will find unified access to the different resources available from the Institute or its collaborators. The resources include: 129S7 and C57BL6/J bacterial artificial chromosomes (BACs), MICER gene targeting vectors, knock-out first conditional-ready gene targeting vectors, embryonic stem (ES) cells with gene targeted mutations or with retroviral gene trap insertions, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen.bacterial artificial chromosome, vector, embryonic stem cell, mutant mouse line, phenotype, 129s7, c57bl6/j, gene, knockout, gene expression, genetics, chromosome, mutant, mouse line, mammal, marker symbolSCR_006239(Sanger Mouse Resources Portal, RRID:SCR_006239)Wellcome Trust Sanger Institute; Hinxton; United Kingdom European Union, NCRR, NHGRI, Wellcome Trustrelated to: Ensembl, Monarch Initiative, listed by: One Mind Biospecimen Bank ListingLast checked downnlx_151819
ScerTFResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceCatalog of over 1,200 position weight matrices (PWMs) for 196 different yeast transcription factors (TFs). They've curated 11 literature sources, benchmarked the published position-specific scoring matrices against in-vivo TF occupancy data and TF deletion experiments, and combined the most accurate models to produce a single collection of the best performing weight matrices for Saccharomyces cerevisiae. ScerTF is useful for a wide range of problems, such as linking regulatory sites with transcription factors, identifying a transcription factor based on a user-input matrix, finding the genes bound/regulated by a particular TF, and finding regulatory interactions between transcription factors. Enter a TF name to find the recommended matrix for a particular TF, or enter a nucleotide sequence to identify all TFs that could bind a particular region.binding site, transcription factor, regulatory site, gene, regulation, regulatory interaction, matrix, nucleotide sequence, dna sequence, yeast, position weight matrixSCR_006121(ScerTF, RRID:SCR_006121)Washington University School of Medicine in St. Louis; Missouri; USA NHGRI, NIGMSlisted by: OMICtoolsPMID:22140105Last checked upnlx_151599, OMICS_00542
LINCS Information FrameworkResource, data or information resource, databaseDatabase for Library of Integrated Network-Based Cellular Signatures (LINCS) data that leverages semantic-web technologies and domain level ontologies. The NIH LINCS program aims to generate an extensive reference set of cellular response signatures to a variety of small molecule and genetic perturbations. The goal is to create a sustainable and widely accessible knowledge resource to advance understanding of the highly orchestrated interplay of molecular biological components in maintaining healthy development and how their perturbation causes disease. The data sets produced at LINCS span a variety of assay formats and technologies, including biochemical and single cell phenotypic responses, and genome-wide transcriptional profiling. This knowledge-based, extensible information system of interconnected components is designed to help scientists to use data and results produced in the LINCS and other NIH screening programs in their own research and to support their translation towards the development of novel therapeutics.bioassay, cell, small molecule, kinase protein, compound, cell, gene, metadata standard, cell line, primary cell, rnai reagent, rnai, reagent, protein reagent, protein, antibody reagent, antibody, perturbagen, growth factor, ligand, linked data, organ, disease, data setSCR_003937(LINCS Information Framework, RRID:SCR_003937)University of Miami; Florida; USA NHGRI, NHLBIrelated to: Broad Institute, Harvard Medical School, Massachusetts, USA, Columbia University, New York, USA, Yale University, Connecticut, USA, Arizona State University, Arizona, USA, uses: HMS LINCS Database, Bioassay Ontology, Molecular Libraries ProgramLast checked upnlx_158348
BioDepot-workflow-builderResource, software resource, software application, workflow software, data processing softwareSoftware tool to create and execute reproducible bioinformatics workflows using drag and drop interface. Graphical widgets represent Docker containers executing modular task. Widgets are linked graphically to build bioinformatics workflows that can be reproducibly deployed across different local and cloud platforms. Each widget contains form-based user interface to facilitate parameter entry and console to display intermediate results.bioinformatics, big, data, workflow, reproducible, DockerSCR_017402(BioDepot-workflow-builder, RRID:SCR_017402)NHGRI, NHLBI, NIGMSDOI:10.1101/099010Last checked up
BioStarResource, forum, discussion, narrative resource, portal, community building portal, data or information resourceA question answer forum for scientists, focusing on methods in bioinformatics, computational genomics and biological data analysis. They welcome detailed and specific posts, written clearly and simply.bioinformatics, computational genomics, biological data analysis, data analysis, forum, question, answerSCR_002580(BioStar, RRID:SCR_002580)Luma Education, NHGRI, NIHrelated to: NeuroStars, listed by: OMICtoolsPMID:22046109Last checked upnlx_155982, OMICS_01706
GalaxyResource, organization portal, production service resource, analysis service resource, data analysis service, service resource, portal, software resource, data or information resourceOpen, web-based platform providing bioinformatics tools and services for data intensive genomic research. Platform may be used as a service or installed locally to perform, reproduce, and share complete analyses. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. The Galaxy team is a part of BX at Penn State, and the Biology and Mathematics and Computer Science departments at Emory University.bioinformatics, workflow, analysis, data sharing, visualization, cloud, genomics, metagenomics, next-generation sequencing, platform, data set, genaddiction toolSCR_006281(Galaxy, RRID:SCR_006281)Pennsylvania State University Huck Institutes for the Life Sciences, Institute for CyberScience at Pennsylvania State University, Johns Hopkins University, NHGRI, NSF, Pennsylvania, Pennsylvania Department of Health, USArelated to: ABrowse, TRAMS, Stem Cell Commons, Stem Cell Discovery Engine, CardioVascular Research Grid (CVRG), rQuant, SnpEff, Binding and Expression Target Analysis, PIPE-CLIP, Stem Cell Discovery Engine, Computational Genomics Analysis Tools, SpliceTrap, SMAGEXP, used by: Nebula, listed by: OMICtools, 3DVC, lists: PathwayMatcher, works_with: DeeptoolsReferences (3)Last checked upnlx_151896, OMICS_01141
Pathway CommonsResource, web service, software resource, data or information resource, data access protocol, databaseDatabase of publicly available pathways from multiple organisms and multiple sources represented in a common language. Pathways include biochemical reactions, complex assembly, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes. Pathways were downloaded directly from source databases. Each source pathway database has been created differently, some by manual extraction of pathway information from the literature and some by computational prediction. Pathway Commons provides a filtering mechanism to allow the user to view only chosen subsets of information, such as only the manually curated subset. The quality of Pathway Commons pathways is dependent on the quality of the pathways from source databases. Pathway Commons aims to collect and integrate all public pathway data available in standard formats. It currently contains data from nine databases with over 1,668 pathways, 442,182 interactions,414 organisms and will be continually expanded and updated. (April 2013)biological pathway, pathway, molecule, biopax, standard exchange formatSCR_002103(Pathway Commons, RRID:SCR_002103)University of Toronto; Ontario; Canada Cancer Biomedical Informatics Grid, NHGRI, NIGMSrelated to: cPath, BioGRID, IntAct, Reactome, MINT, HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism, Cancer Cell Map, HPRD - Human Protein Reference Database, Integrated Molecular Interaction Database, Pathway Interaction Database, CHEBI, Universal Protein Resource, PANTHER, WebGestalt: WEB-based GEne SeT AnaLysis ToolkitPMID:21071392Last checked downnif-0000-20884
Consensus Measures for Phenotype and ExposureResource, knowledge environmentPhenX 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, researchSCR_006688(Consensus Measures for Phenotype and Exposure, RRID:SCR_006688)RTI International NHGRILast checked upnif-0000-32816
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