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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
VirusHunter
 
Resource Report
Resource Website
VirusHunter (RRID:SCR_001198) VirusHunter software resource A fully automated and modular software package for mining sequence data to identify sequences of microbial origin. The pipeline was optimized for analysis of data generated by the Roche/454 next-generation sequencing platform but can be applied to longer sequences (Sanger sequencing data or assembled contigs) as well. Microbial sequences are identified on the basis of BLAST alignments and the taxonomic classification of the reference sequence(s) to which a read is aligned. Viruses are the focal point of VirusHunter as released, but it can be easily modified to generate parallel outputs for bacterial or parasitic species. To date, VirusHunter has been applied to thousands of specimens, including human, animal and environmental samples, resulting in the detection of many known and novel viruses. virus, next-generation sequencing, roche, 454, taxonomic classification, alignment, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA
PMID:24167629 THIS RESOURCE IS NO LONGER IN SERVICE biotools:virushunter, OMICS_02153 https://bio.tools/virushunter SCR_001198 2026-02-14 01:59:55 0
Genome Trax
 
Resource Report
Resource Website
1+ mentions
Genome Trax (RRID:SCR_001234) Genome Trax service resource Service that provides a comprehensive compilation of variant knowledge that allows you to identify pathogenic variants in human whole genome or exome sequences. It makes it easy to upload a complete genome?s worth of variations and identify the biologically relevant subset of known mutations, mutations that are novel and appear in a candidate disease genes, or mutations that are predicted to have a deleterious effect. The database includes a comprehensive collection of disease causing mutations from HGMD Professional, regulatory sites from TRANSFAC , and disease genes, drug targets and pathways from PROTEOME, as well as pharmacogenomic variants. It integrates the best public data-sets on somatic mutations, allele frequencies and clinical variants, in their most up-to-date version, for a total of more than 165 million annotations. It is possible to identify known pathogenic variants, remove harmless common variants, and obtain deleterious predictions for novel variants. With family data, it is possible to identify variants that are de novo, compound heterozygous only in the offspring. All of the results can be downloaded to Excel for further review. For core facilities and bioinformaticians, the complete underlying data is made available for download and easy integration into custom analysis pipelines. Genome Trax data is optimized to work with many other software packages, such as ANNOVARTM, CLC bio, Alamut, SimulConsult, and Cartagenia. next-generation sequencing, genome, exome, sequence, variation, mutation, pathogenic, database, bio.tools, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: BIOBASE Corporation
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_02109, biotools:genome_trax https://bio.tools/genome_trax SCR_001234 Genome Trax for Next Generation Sequencing 2026-02-14 01:59:58 2
ITALICS
 
Resource Report
Resource Website
ITALICS (RRID:SCR_001274) ITALICS software resource Software package to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set. affymetrix, copy number variation, microarray is listed by: OMICtools
has parent organization: Bioconductor
PMID:18252739 Free, Available for download, Freely available OMICS_02064 SCR_001274 2026-02-14 01:59:59 0
DEXUS
 
Resource Report
Resource Website
1+ mentions
DEXUS (RRID:SCR_001309) DEXUS software resource Software package that identifies differentially expressed genes in RNA-Seq data under all possible study designs such as studies without replicates, without sample groups, and with unknown conditions. It works also for known conditions, for example for RNA-Seq data with two or multiple conditions. RNA-Seq read count data can be provided both by the S4 class Count Data Set and by read count matrices. Differentially expressed transcripts can be visualized by heatmaps, in which unknown conditions, replicates, and samples groups are also indicated. This software is fast since the core algorithm is written in C. For very large data sets, a parallel version of DEXUS is provided in this package. DEXUS is a statistical model that is selected in a Bayesian framework by an EM algorithm. It does not need replicates to detect differentially expressed transcripts, since the replicates (or conditions) are estimated by the EM method for each transcript. The method provides an informative/non-informative value to extract differentially expressed transcripts at a desired significance level or power. classification, differential expression, gene expression, hapmap, quality control, rna-seq, sequencing, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Bioconductor
PMID:24049071 Free, Available for download, Freely available biotools:dexus, OMICS_02024 http://www.bioconductor.org/packages/release/bioc/html/dexus.html SCR_001309 DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates 2026-02-14 02:00:00 1
Center for Biomedical OCT Research
 
Resource Report
Resource Website
1+ mentions
Center for Biomedical OCT Research (RRID:SCR_001418) CBORT training resource Biomedical technology research center that pioneers and provides access to microscopic imaging instruments for biologic and clinical research. Optical coherence tomography (OCT) has evolved over the last two decades to become a standard of care for diagnostic ophthalmic imaging and is poised to make significant impact in the fields of cardiology and gastrointestinal endoscopy. Access to state-of-the-art instrumentation, however, has been limited to a relatively few research laboratories and the optimization of instruments for new biomedical applications has hindered the investigation of new opportunities. A major focus of CBORT will be to cultivate strategic research collaborations and respond to a pressing need for application-specific OCT instrumentation and hardware. imaging, optical coherence tomography, microscope, catheter, endoscopy, near infrared fluorescence has parent organization: Harvard Medical School; Massachusetts; USA NIBIB P41EB015903 Free, Freely Available nlx_152640 SCR_001418 Center for Biomedical OCT Research and Translation 2026-02-14 02:00:03 2
Flash Gviewer
 
Resource Report
Resource Website
1+ mentions
Flash Gviewer (RRID:SCR_012870) Flash GViewer software resource Flash GViewer is a customizable Flash movie that can be easily inserted into a web page to display each chromosome in a genome along with the locations of individual features on the chromosomes. It is intended to provide an overview of the genomic locations of a specific set of features - eg. genes and QTLs associated with a specific phenotype, etc. rather than as a way to view all features on the genome. The features can hyperlink out to a detail page to enable to GViewer to be used as a navigation tool. In addition the bands on the chromosomes can link to defineable URL and new region selection sliders can be used to select a specific chromosome region and then link out to a genome browser for higher resolution information. Genome maps for Rat, Mouse, Human and C. elegans are provided but other genome maps can be easily created. Annotation data can be provided as static text files or produced as XML via server scripts. This tool is not GO-specific, but was built for the purpose of viewing GO annotation data. Platform: Online tool visualization, chromosome, video, gene, qtl, genome, navitgation, phenotype, ontology or annotation visualization is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: Medical College of Wisconsin; Wisconsin; USA
Free for academic use nlx_149333 http://gmod.org/flashgviewer SCR_012870 2026-02-14 02:02:24 2
Children and Adults with Attention Deficit/Hyperactivity Disorder
 
Resource Report
Resource Website
1+ mentions
Children and Adults with Attention Deficit/Hyperactivity Disorder (RRID:SCR_013384) CHADD nonprofit organization Non-profit organization serving individuals with attention deficit-hyperactivity disorder (AD/HD) and their families. CHADD has over 16,000 members in 200 local chapters throughout the U.S. Chapters offer support for individuals, parents, teachers, professionals, and others. CHADD''s primary objectives are: to provide a support network for parents and caregivers; to provide a forum for continuing education; to be a community resource and disseminate accurate, evidence-based information about AD/HD to parents, educators, adults, professionals, and the media; to promote ongoing research; and to be an advocate on behalf of the AD/HD community. In general, CHADD works to improve the lives of people affected by AD/HD through: Collaborative Leadership, Advocacy, Research Education and, Support CHADD has three current priority objectives: (1) to serve as a clearinghouse for evidence-based information on AD/HD, (2) to serve as a local face-to-face family support group for families and individuals affected by AD/HD, and (3) to serve as an advocate for appropriate public policies and public recognition in response to needs faced by families and individuals with AD/HD. CHADD is a membership organization, produces the bi-monthly Attention! magazine (for members), and sponsors an annual conference. The National Resource Center on AD/HD (NRC) is the CDC-funded national clearinghouse for evidence-based information about AD/HD. education, family, adult human, advocacy, attention, attention deficit disorder, caregiver, child, deficit, disorder, hyperactivity, hyperactivity disorder, individual, media, medication, news, parent, professional, research, support, teacher, treatment, young human Attention deficit-hyperactivity disorder ISNI: 0000 0004 0546 7056, nif-0000-10195, grid.433005.1 https://ror.org/01ds3sh29 SCR_013384 2026-02-14 02:02:51 2
National Drug Code Directory
 
Resource Report
Resource Website
National Drug Code Directory (RRID:SCR_013721) ndc Drug database published by the Food and Drug Administration of unique universal product identifiers for all drugs manufactured, prepared, propagated, compounded, or processed by it for commercial distribution. drug database, drug code, FDA Free, public SCR_013721 2026-02-14 02:02:30 0
Approved Drug Products with Therapeutic Equivalence Evaluations
 
Resource Report
Resource Website
1+ mentions
Approved Drug Products with Therapeutic Equivalence Evaluations (RRID:SCR_013727) Orange Book Database that contains drug products approved on the basis of safety and effectiveness by the Food and Drug Administration. drugs, prescription drug, over-the-counter drug, OTC drug, Drug Products is listed by: U.S. Food and Drug Administration
has parent organization: U.S. Food and Drug Administration
Free, public SCR_013727 2026-02-14 02:02:54 2
Biospecimen Repository and Processing Core
 
Resource Report
Resource Website
Biospecimen Repository and Processing Core (RRID:SCR_013792) BRPC information resource A biomaterial supply and access service resource which provides a shared resource for coordinated tissue processing and biorepository services. Services include patient identification and informed consent, specimen collection, processing and banking, and annotation of banked specimens and specimen distribution. They provide biospecimen inventory management, services, and equipment. It is a shared resource of Duke University. repository, biomaterial supply resource, shared resource, Duke University, biospecimen, tissue, tissue processing, informed consent, biobank is related to: Duke Cancer Institute
is related to: Duke Biobank
is related to: Duke University School of Medicine; North Carolina; USA
has parent organization: Duke University; North Carolina; USA
Available to the research and education community, Fee http://www.dukecancerinstitute.org/research/shared-resources/Biospecimen%20Repository%20and%20Processing%20Core SCR_013792 2026-02-14 02:02:34 0
National Database for Clinical Trials related to Mental Illness
 
Resource Report
Resource Website
1+ mentions
National Database for Clinical Trials related to Mental Illness (RRID:SCR_013795) NDCT data resource A database which houses human subjects clinical trial data. NDCT currently contains data on 13,409 subjects and has access to data on 100,500 subjects from the NIMH Data Archive. Users can also sign up for news updates and watch video tutorials. database, human, clinical trial, mental health, mental illness uses: NIMH Data Archive
uses: RDoCdb
is listed by: NIH Data Sharing Repositories
is related to: NIMH Data Archive
is related to: RDoCdb
is related to: RDoCdb
NIH Public, Only for research SCR_013795 2026-02-14 02:02:51 2
Spatio-temporal transcriptome of the human brain
 
Resource Report
Resource Website
Spatio-temporal transcriptome of the human brain (RRID:SCR_013743) data or information resource, document, narrative resource A research paper with supplementary materials reporting the generation and analysis of exon-level transcriptome and associated genotyping data. The experiment represented both males and females of multiple ethnicities and examines gene regulation and expression in different areas of the brain. A data set on the human brain transcriptome as well as insights into the transcriptional foundations of human neurodevelopment is provided. spatio-temporal, transcriptome data, brain regions, human brain, gene expression, gene regulation is related to: Human Brain Transcriptome
has parent organization: Yale University; Connecticut; USA
Kavil Foundation ;
NARSAD ;
James S. McDonnell Foundation Scholar Award ;
NIMH MH081896;
NIMH MH089929;
NINDS NS054273
PMID:22031440 Public, Free SCR_013743 2026-02-14 02:02:50 0
NIMH Repository and Genomics Resources
 
Resource Report
Resource Website
50+ mentions
NIMH Repository and Genomics Resources (RRID:SCR_006698) NRGR, RGR institution Collaborative venture between the National Institute of Mental Health (NIMH) and several academic institutions. Repository facilitates psychiatric genetic research by providing patient and control samples and phenotypic data for wide-range of mental disorders and Stem Cells.Stores biosamples, genetic, pedigree and clinical data collected in designated NIMH-funded human subject studies. RGR database likewise links to other repositories holding data from same subjects, including dbGAP, GEO and NDAR. Allows to access these data and biospecimens (e.g., lymphoblastoid cell lines, induced pluripotent cell lines, fibroblasts) and further expand genetic and molecular characterization of patient populations with severe mental illness. biosamples, genetic, pedigree, clinical, data is listed by: One Mind Biospecimen Bank Listing
is related to: NIMH Stem Cell Center
is related to: Rutgers Cell and DNA Repository
is related to: Sequenced Treatment Alternatives to Relieve Depression Study
is related to: CATIE - Clinical Antipsychotic Trials in Intervention Effectiveness
is related to: Systematic Treatment Enhancement Program for Bipolar Disorder (STEP-BD)
is related to: NKI-RS Enhanced Sample
has parent organization: Rutgers University; New Jersey; USA
has parent organization: Washington University in St. Louis; Missouri; USA
has parent organization: University of Southern California; Los Angeles; USA
Bipolar Disorder, Schizophrenia, Alzheimer's disease, Autism, Attention deficit-hyperactivity disorder, Depression, Control, Obsessive-Compulsive Disorder, Anorexia Nervosa, Relative, Mental disorder, Brain disorder, Relative NIH Blueprint for Neuroscience Research ;
National Institute for Mental Health
Restricted grid.482687.7, nif-0000-00186, SCR_016318 https://ror.org/026dax180 SCR_006698 NIMH: Center for Collaborative Genetic Studies, NIMH Human Genetics Initiative, NIMH Center for Genetic Studies, NIMH Genetics, Center for Collaborative Genomic Studies on Mental Disorders, NIMH Repository and Genomics Resources (NRGR) 2026-02-14 02:01:14 66
GREC Corpus
 
Resource Report
Resource Website
1+ mentions
GREC Corpus (RRID:SCR_006719) GREC training set A semantically annotated corpus of 240 MEDLINE abstracts (167 on the subject of E. coli species and 73 on the subject of the Human species) intended for training information extraction (IE) systems and/or resources which are used to extract events from biomedical literature. The corpus has been manually annotated with events relating to gene regulation by biologists. Each event is centered on either a verb (e.g. transcribe) or nominalized verb (e.g. transcription) and annotation consists of identifying, as exhaustively as possible, the structurally-related arguments of the verb or nominalized verb within the same sentence. Each event argument is then assigned the following information: * A semantic role from a fixed set of 13 roles which are tailored to the biomedical domain. * A biomedical concept type (where appropriate). The corpus in available for download in 2 formats: * A standoff format, based on the BioNLP'09 Shared Task format * An XML format, based on the GENIA event annotation format annotation, information extraction, text mining, semantic role, semantic search, gene, computational linguistics, gene regulation is listed by: FORCE11
is related to: MEDLINE
has parent organization: National Centre for Text Mining
JISC PMID:19852798 Creative Commons Attribution-NonCommercial-ShareAlike License, v3 Unported, For Copyright of abstracts refer to PubMed. nif-0000-06688 SCR_006719 Gene Event Regulation Corpus 2026-02-14 02:01:12 3
InnateDB
 
Resource Report
Resource Website
100+ mentions
InnateDB (RRID:SCR_006714) InnateDB data or information resource, database Publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralized resource. The database can be mined as a knowledgebase or used with the integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response. Although InnateDB curation focuses on innate immunity-relevant interactions and pathways, it also incorporates detailed annotation on the entire human, mouse and bovine interactomes by integrating data (178,000+ interactions & 3,900+ pathways) from several of the major public interaction and pathway databases. InnateDB also has integrated human, mouse and bovine orthology predictions generated using Ortholgue software. Ortholgue uses a phylogenetic distance-based method to identify possible paralogs in high-throughput orthology predictions. Integrated human and mouse conserved gene order and synteny information has also been determined to provide further support for orthology predictions. InnateDB Capabilities: * View statistics for manually-curated innate immunity relevant molecular interactions. New manually curated interactions are submitted weekly. * Search for genes and proteins of interest. * Search for experimentally-verified molecular interactions by gene/protein name, interaction type, cell type, etc. * Search genes/interactions belonging to 3,900 pathways. * Visualize interactions using an intuitive subcellular localization-based layout in Cerebral. * Upload your own list of genes along with associated gene expression data (from up to 10 experimental conditions) to interactively analyze this data in a molecular interaction network context. Once you have uploaded your data, you will be able to interactively visualize interaction networks with expression data overlaid; carry out Pathway, Gene Ontology and Transcription Factor Binding Site over-representation analyses; construct orthologous interaction networks in other species; and much more. * Access curated interaction data via a dedicated PSICQUIC webservice. gene, immune response, pathway, protein, signaling pathway, interaction, immune, signaling response, gene, orthology prediction, orthology, ortholg, annotation, interactome, gene expression, molecule, protein-protein interaction, molecular interaction, visualization, nucleic acid-protein, nucleic acid, network, web service, transcription factor binding site, software resource, FASEB list is listed by: re3data.org
is related to: IMEx - The International Molecular Exchange Consortium
is related to: Interaction Reference Index
is related to: ConsensusPathDB
is related to: IMEx - The International Molecular Exchange Consortium
is related to: PSICQUIC Registry
is related to: PSICQUIC Registry
is related to: Gene Ontology
is related to: IntAct
has parent organization: Simon Fraser University; British Columbia; Canada
has parent organization: University of British Columbia; British Columbia; Canada
works with: IMEx - The International Molecular Exchange Consortium
Microbial infection, Allergy, Asthma Michael Smith Foundation for Health Research ;
AllerGen 12ASI1;
AllerGen 12B&B2;
Teagasc RMIS6018;
European Union PSIMEx project contract FP7-HEALTH-2007-223411
PMID:23180781
PMID:18766178
Free, Freely available nif-0000-20808, r3d100010676 https://doi.org/10.17616/R36S43 SCR_006714 A Knowledge Resource for Innate Immunity Interactions and Pathways, InnateDB: Systems Biology of the Innate Immune Response, InnateDB - A Knowledge Resource for Innate Immunity Interactions and Pathways 2026-02-14 02:01:14 496
University of Quebec Hospital Centre; Quebec; Canada
 
Resource Report
Resource Website
University of Quebec Hospital Centre; Quebec; Canada (RRID:SCR_006740) CHUQ university Network of three teaching hospitals affiliated with the medical school of Université Laval and several specialized institutions in Quebec City. is related to: Cancer Research Network of the FRSQ
has parent organization: Laval University; Quebec; Canada
Wikidata:Q3145390, nlx_158566, grid.417661.3, ISNI:0000 0001 2190 0479 https://ror.org/034sbqc84 SCR_006740 University of Quebec Hospital Center, University of Quebec Hospital Centre, CHU de Qu�bec, Centre hospitalier universitaire de Quebec, CHU de Quebec, Centre hospitalier universitaire de Qu�bec 2026-02-14 02:01:12 0
National Institute of Child Health and Human Development
 
Resource Report
Resource Website
100+ mentions
National Institute of Child Health and Human Development (RRID:SCR_011429) NICHD institution A national institute that investigates human development throughout the entire life process, focusing on understanding developmental disabilities, including intellectual and developmental disabilities, and illuminating important events that occur during pregnancy. The NICHD conducts and supports laboratory research, clinical trials, and epidemiological studies that explore health processes; examines the impact of disabilities, diseases, and defects on the lives of individuals; and sponsors training programs for scientists, doctors, and researchers to ensure that NICHD research can continue. The Institute also supports research training across all its programs. In addition, an overarching responsibility of the NICHD is to disseminate information that emanates from Institute research programs to researchers, practitioners, other health care professionals, and the public. human development, developmental disabilities, pregnancy, national institute has parent organization: NIH Blueprint for Neuroscience Research
has parent organization: National Institutes of Health
is parent organization of: NICHD Developmental Neuroethology - Laboratory of Comparative Ethology
is parent organization of: TORTOISE
is parent organization of: NCMRR - National Center for Medical Rehabilitation Research
is parent organization of: GermSAGE
is parent organization of: Traumatic Brain Injury Clinical Trials Network
Available to the research community nlx_inv_1005104, Crossref funder ID: 100000071, Wikidata: Q5409765, grid.420089.7, ISNI: 0000 0000 9635 8082 https://ror.org/04byxyr05 SCR_011429 Eunice Kennedy Shriver National Institute of Child Health and Human Development 2026-02-14 02:02:18 165
Seattle Childrens Research Institute; Washington; USA
 
Resource Report
Resource Website
1+ mentions
Seattle Childrens Research Institute; Washington; USA (RRID:SCR_011520) institution A top five pediatric research center in the nation that brings together the best minds in pediatric research to set new standards of pediatric care and find new cures for childhood diseases. Their goal is that every patient at Seattle Children''s has the opportunity to participate in, or benefit from, their groundbreaking research. The research institute is organized into nine centers, each one specializing in areas like cancer immunotherapy, neuroscience and child health and behavior. The centers are supported by faculty from the Treuman Katz Center for Pediatric Bioethics , the nation''s first pediatric bioethics center. is related to: Beta Cell Biology Consortium
is parent organization of: Seattle Children's Research Institute Micro Computed Tomography Imaging and Visualization Lab Core Facility
is parent organization of: Seattle Childrens Research Institute Behavioral Phenotyping Core Facility
nlx_158444 SCR_011520 Seattle Childrens Research Institute, Seattle Children''s Research Institute 2026-02-14 02:02:21 1
University of Montreal Hospital Centre; Quebec; Canada
 
Resource Report
Resource Website
University of Montreal Hospital Centre; Quebec; Canada (RRID:SCR_011686) CHUM university Hôpital Saint-Luc was a hospital in Montreal, Quebec, Canada, at the intersection of Saint Denis Street and René Lévesque Boulevard in the borough of Ville-Marie. It was named in honor of Luke the Evangelist, who is the patron saint of doctors in the Roman Catholic religion. is related to: Cancer Research Network of the FRSQ
has parent organization: University of Montreal; Quebec; Canada
Wikidata:Q1054216, ISNI:0000 0001 0743 2111, nlx_158565, grid.410559.c https://ror.org/0410a8y51 SCR_011686 Montreal University Health Centre, University of Montreal Hospital Centre, University of Montreal Hospital Center, Centre hospitalier de l''Universite de Montreal, Montreal University Hospital Centre, Centre hospitalier de l''Universit� de Montr�al, Montreal University Hospital Center 2026-02-14 02:02:25 0
Vestische Children and Youth Clinic Dates; North Rhine-Westphalia; Germany
 
Resource Report
Resource Website
Vestische Children and Youth Clinic Dates; North Rhine-Westphalia; Germany (RRID:SCR_011759) hospital is related to: EMIF
has parent organization: Witten/Herdecke University; North Rhine-Westphalia; Germany
SCR_011759 Vestische Kinder- und Jugendklinik Datteln, Vestische Children and Youth Clinic Dates 2026-02-14 02:02:26 0

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