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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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EPIMHC Resource Report Resource Website 1+ mentions |
EPIMHC (RRID:SCR_016279) | data or information resource, database | Database of naturally processed MHC-restricted peptide ligands and epitopes for customized computational vaccinology. | mhc, peptide, ligand, eiptope, vaccine, vaccinology, virology, t cell, immunogenic, molecule, virus | NIAID AI50900; NIAID AI43649; Molecular Immunology Foundation |
PMID:15657103 | Freely available, The research community can contribute to this resource | SCR_016279 | EPIMHC Database | 2026-02-11 10:59:29 | 4 | ||||||||
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Database of Antimicrobial Activity and Structure of Peptides Resource Report Resource Website 10+ mentions |
Database of Antimicrobial Activity and Structure of Peptides (RRID:SCR_016600) | DBAASP | data or information resource, database | Collection of manually curated data regarding structure and antimicrobial activity of natural and synthetic peptides. Provides the information and analytical resources to develop antimicrobial compounds with the high therapeutic index. | data, collection, structure, antimicrobial, activity, natural, synthetic, peptide, sequence | NIAID G2102; Shota Rustaveli National Science Foundation FR397718014; International Science and Technology Center |
PMID:26578581 PMID:27060142 |
Free, Freely available | SCR_016600 | DataBase of Antimicrobial Activity and Structure of Peptides, Database of Antimicrobial Activity and Structure of Peptides | 2026-02-11 10:59:27 | 42 | |||||||
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ImmGen Resource Report Resource Website 100+ mentions |
ImmGen (RRID:SCR_021792) | data or information resource, database | Project combines immunology and computational biology laboratories in effort to establish complete road map of gene-expression and regulatory networks in all immune cells. Project will generate, with rigorously standardized conditions, complete compendium of genome-wide data sets showing expression of protein-coding genes for all defined cell populations of mouse immune system. | gene expression, regulatory networks, all immune cells, protein coding genes, mouse immune system | NIAID R24 AI072073 | PMID:18800157 PMID:32978299 |
Free, Freely available | SCR_021792 | Immunological Genome Project | 2026-02-11 11:00:11 | 258 | ||||||||
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CharProtDB: Characterized Protein Database Resource Report Resource Website |
CharProtDB: Characterized Protein Database (RRID:SCR_005872) | CharProtDB | data or information resource, database | The Characterized Protein Database, CharProtDB, is designed and being developed as a resource of expertly curated, experimentally characterized proteins described in published literature. For each protein record in CharProtDB, storage of several data types is supported. It includes functional annotation (several instances of protein names and gene symbols) taxonomic classification, literature links, specific Gene Ontology (GO) terms and GO evidence codes, EC (Enzyme Commisssion) and TC (Transport Classification) numbers and protein sequence. Additionally, each protein record is associated with cross links to all public accessions in major protein databases as ��synonymous accessions��. Each of the above data types can be linked to as many literature references as possible. Every CharProtDB entry requires minimum data types to be furnished. They are protein name, GO terms and supporting reference(s) associated to GO evidence codes. Annotating using the GO system is of importance for several reasons; the GO system captures defined concepts (the GO terms) with unique ids, which can be attached to specific genes and the three controlled vocabularies of the GO allow for the capture of much more annotation information than is traditionally captured in protein common names, including, for example, not just the function of the protein, but its location as well. GO evidence codes implemented in CharProtDB directly correlate with the GO consortium definitions of experimental codes. CharProtDB tools link characterization data from multiple input streams through synonymous accessions or direct sequence identity. CharProtDB can represent multiple characterizations of the same protein, with proper attribution and links to database sources. Users can use a variety of search terms including protein name, gene symbol, EC number, organism name, accessions or any text to search the database. Following the search, a display page lists all the proteins that match the search term. Click on the protein name to view more detailed annotated information for each protein. Additionally, each protein record can be annotated. | protein, annotation, functional annotation, taxonomic classification, literature, gene ontology, evidence code, enzyme commission, transport classification, protein sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: J. Craig Venter Institute |
NHGRI R01 HG004881; NIAID contract HHSN266200100038C |
PMID:22140108 | biotools:charprotdb, nlx_149421 | https://bio.tools/charprotdb | SCR_005872 | Characterized Protein Database | 2026-02-11 10:57:10 | 0 | |||||
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Add Health (National Longitudinal Study of Adolescent Health) Resource Report Resource Website 10+ mentions |
Add Health (National Longitudinal Study of Adolescent Health) (RRID:SCR_007434) | Add Health | data or information resource, database | Longitudinal study of a nationally representative sample of adolescents in grades 7-12 in the United States during the 1994-95 school year. Public data on about 21,000 people first surveyed in 1994 are available on the first phases of the study, as well as study design specifications. It also includes some parent and biomarker data. The Add Health cohort has been followed into young adulthood with four in-home interviews, the most recent in 2008, when the sample was aged 24-32. Add Health combines longitudinal survey data on respondents social, economic, psychological and physical well-being with contextual data on the family, neighborhood, community, school, friendships, peer groups, and romantic relationships, providing unique opportunities to study how social environments and behaviors in adolescence are linked to health and achievement outcomes in young adulthood. The fourth wave of interviews expanded the collection of biological data in Add Health to understand the social, behavioral, and biological linkages in health trajectories as the Add Health cohort ages through adulthood. The restricted-use contract includes four hours of free consultation with appropriate staff; after that, there''s a fee for help. Researchers can also share information through a listserv devoted to the database. | adolescent, longitudinal, adult human, interview, social, behavior, health, early adult human, FASEB list | has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA | Aging | NICHD ; NCI ; CDC ; NIAID ; NIMHD ; NIDCD ; NIGMS ; NIMH ; NINR ; NIA ; NIAAA ; NIDA ; NSF ; NIH ; Department of Health and Human Services ; MacArthur Foundation ; Robert Wood Johnson Foundation |
Restricted use | nif-0000-00621 | SCR_007434 | National Longitudinal Study of Adolescent Health | 2026-02-11 10:57:35 | 37 | |||||
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ApiDots Resource Report Resource Website 1+ mentions |
ApiDots (RRID:SCR_001778) | data or information resource, database | Note: ApiDots is currently unavailable. For data on apicomplexan EST assemblies, please see EuPathDB ApiDots is a database integrating mRNA/EST sequences from numerous Apicomplexan parasites. ESTs and mRNAs were clustered and further assembled to generate consensus sequences. These consensus sequences were then subjected to database searches against protein sequences and protein domain sequences. The underlying relational structure of this database allows researchers to analyze these data and pose biologically interesting questions. | est, apicomplexan parasite, mrna, protein domain sequence, protein sequence |
is related to: Eukaryotic Pathogen Database Resources has parent organization: University of Pennsylvania; Philadelphia; USA |
USDA ; Amerman Family Foundation ; Merck Research Laboratories ; Burroughs Wellcome Fund ; NRI 99-35204-8615; NIAID AI45806; NIAID AI45806A1; NIAID AI48121 |
PMID:12618375 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02556 | SCR_001778 | 2026-02-11 10:56:18 | 2 | |||||||
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Nonhuman Primate HIV/SIV Vaccine Trials Database Resource Report Resource Website |
Nonhuman Primate HIV/SIV Vaccine Trials Database (RRID:SCR_002274) | data or information resource, database | An overview of HIV and SIV vaccine trials and their outcomes. It was developed as a tool for compilation, search and comparison of published studies on SIV, HIV and SHIV vaccine trials in nonhuman primates. We used a set of criteria to scan Pubmed for relevant studies to enter into the database. In selecting studies for entry, priority was given to recently published studies in journals generally regarded as the primary source of information pertaining to HIV and SIV vaccine research in nonhuman primates. In most cases, we give priority to challenge studies, where the animals received a live virus to measure the "efficacy" of the immunogen(s) inoculated during the course of the investigation. The HIV Sequence Database focuses on five primary goals: *Collecting HIV and SIV sequence data (all sequences since 1987) *Curating and annotating this data, and making it available to the scientific community *Computer analysis of HIV and related sequences *Production of software for the analysis of (sequence) data *Publication of the data and analyses on this site and in a yearly printed publication, the HIV sequence Compendium, which is available free of charge | drug, trial, vaccine, human immunodeficiency virus, simian immunodeficiency virus | has parent organization: HIV Databases | Human immunodeficiency virus, Simian immunodeficiency virus | NIAID | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20999 | http://hiv-web.lanl.gov/cgi-bin/vaccine/public/index.cgi | SCR_002274 | HIV/SIV Trials Vaccine DB, HIV/SIV Trials Vaccine Database | 2026-02-11 10:56:26 | 0 | |||||
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HIV Molecular Immunology Database Resource Report Resource Website 1+ mentions |
HIV Molecular Immunology Database (RRID:SCR_002893) | HIV Molecular Immunology Database | data or information resource, database | An annotated, searchable collection of HIV-1 cytotoxic and helper T-cell epitopes and antibody binding sites, plus related tools and information. The goal of this database is to provide a comprehensive listing of defined HIV epitopes. These data are also printed in the HIV Molecular Immunology compendium, which is updated yearly and provided free of charge to scientific researchers, both by online download and as a printed copy. The data included in this database are extracted from the HIV immunology literature. HIV-specific B-cell and T-cell responses are summarized and annotated. Immunological responses are divided into three sections, CTL (CD8+), T helper (CD4+), and antibody. Within these sections, defined epitopes are organized by protein and binding sites within each protein, moving from left to right through the coding regions spanning the HIV genome. We include human responses to natural HIV infections, as well as vaccine studies in a range of animal models and human trials. Responses that are not specifically defined, such as responses to whole proteins or monoclonal antibody responses to discontinuous epitopes, are summarized at the end of each protein sub-section. Studies describing general HIV responses to the virus, but not to any specific protein, are included at the end of each section. The annotation includes information such as cross-reactivity, escape mutations, antibody sequence, TCR usage, functional domains that overlap with an epitope, immune response associations with rates of progression and therapy, and how specific epitopes were experimentally defined. Basic information such as HLA specificities for T-cell epitopes, isotypes of monoclonal antibodies, and epitope sequences are included whenever possible. All studies that we can find that incorporate the use of a specific monoclonal antibody are included in the entry for that antibody. A single T-cell epitope can have multiple entries, generally one entry per study. Finally, tables and maps of all defined linear epitopes relative to the HXB2 reference proteins are provided. Alignments of CTL, helper T-cell, and antibody epitopes are available through the search interfaces. Only responses to HIV-1 and HIV-2 are included in the database. | cytotoxic t cell, cytotoxic t lymphocyte, helper t-cell, antibody, binding site, epitope, t cell epitope, human immunodeficiency virus, immunology, molecule, genome, protein, alignment, b-cell, t-cell, annotation, ctl, t helper, coding region, cross-reactivity, escape mutation, antibody sequence, tcr usage, functional domain, immune response, progression, therapy | has parent organization: HIV Databases | Human immunodeficiency virus | NIAID | nif-0000-02965 | http://hiv-web.lanl.gov/immunology/ | SCR_002893 | Human Immunodeficiency Virus Molecular Immunology Database | 2026-02-11 10:56:33 | 2 | |||||
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Malaria Parasite Metabolic Pathways Resource Report Resource Website 10+ mentions |
Malaria Parasite Metabolic Pathways (RRID:SCR_007072) | Malaria Parasite Metabolic Pathways | data or information resource, image collection, data set | Data set of metabolic pathways for the malaria parasite based on the present knowledge of parasite biochemistry and on pathways known to occur in other unicellular eukaryotes. This site extracted the pertinent information from the universal sites and presented them in an educative and informative format. The site also includes, cell-cell interactions (cytoadherence and rosetting), invasion of the erythrocyte by the parasite and transport functions. It also contains an artistic impression of the ultrastructural morphology of the interaerythrocytic cycle stages and some details about the morphology of mitochondria and the apicoplast. Most pathways are relevant to the erythrocytic phase of the parasite cycle. All maps were checked for the presence of enzyme-coding genes as they are officially annotated in the Plasmodium genome (http://plasmodb.org/). The site is constructed in a hierarchical pattern that permits logical deepening: * Grouped pathways of major chemical components or biological process ** Specific pathways or specific process *** Chemical structures of substrates and products or process **** Names of enzymes and their genes or components of process Each map is linked to other maps thus enabling to verify the origin of a substrate or the fate of a product. Clicking on the EC number that appears next to each enzyme, connects the site to BRENDA, SWISSPROT ExPASy ENZYME, PlasmoDB and to IUBMB reaction scheme. Clicking of the name of a metabolite, connects the site to KEGG thus providing its chemical structure and formula. Next to each enzyme there is a pie that depicts the stage-dependent transcription of the enzyme''s coding gene. The pie is constructed as a clock of the 48 hours of the parasite cycle, where red signifies over-transcription and green, under-transcription. Clicking on the pie links to the DeRisi/UCSF transcriptome database. | enzyme, gene, genome, map, metabolic, mosquito, parasite, pathway, plasmodium falciparum, protein, reaction, sequence, metabolic pathway, chemical structure, cell-cell interaction, transport, morphology, mitochondria, apicoplast | has parent organization: Hebrew University of Jerusalem; Jerusalem; Israel | Malaria | UNDP/World Bank/WHO Special Programme ; NIAID ; European Union ; 6th FP- BioMalPar Network of Excellence on Biology and Pathology of the Malaria Parasite |
nif-0000-21249 | SCR_007072 | 2026-02-12 09:44:27 | 20 | |||||||
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E. coli Genome project Resource Report Resource Website 1+ mentions |
E. coli Genome project (RRID:SCR_008139) | data or information resource, portal, database, topical portal | The E. coli Genome Project has the goal of completely sequencing the E. coli and human genomes. They began isolation of an overlapping lambda clonebank of E. coli K-12 strain MG1655. Those clones served as the starting material in our initial efforts to sequence the whole genome. Improvements in sequencing technology have since reached the point where whole-genome sequencing of microbial genomes is routine, and the human genome has in fact been completed. They initiated additional sequencing efforts, concentrating on pathogenic members of the family Enterobacteriaceae -- to which E. coli belongs. They also began a systematic functional characterization of E. coli K-12 genes and their regulation, using the whole genome sequence to address how the over 4000 genes of this organism act together to enable its survival in a wide range of environments. | e. coli, enterobcteriaceae, gene, genome, human, journal aricle, knowledgebase, regulation, sequence, job | has parent organization: University of Wisconsin-Madison; Wisconsin; USA | NIAID ; NHGRI |
nif-0000-20961 | SCR_008139 | E.Coli genome project | 2026-02-12 09:44:46 | 5 | ||||||||
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Immune Disorder Ontology Resource Report Resource Website |
Immune Disorder Ontology (RRID:SCR_010344) | IMMDIS | data or information resource, ontology, controlled vocabulary | Ontology generated as part of the Bioinformatics Integration Support Contract (BISC) that is based on the National Library of Medicine (NLM) Medical Subject Headings; National Cancer Institute Thesaurus; International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM); ICD-10; and other open source public databases. Specific information may be available about a class, including Preferred_Name, DEFINITION, Synonym, etc. | obo, health, immunology | is listed by: BioPortal | NIAID ; Division of Allergy Immunology and Transplantation |
nlx_157438 | SCR_010344 | 2026-02-12 09:45:09 | 0 | ||||||||
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HIV Sequence Database Resource Report Resource Website 100+ mentions |
HIV Sequence Database (RRID:SCR_002906) | HIV Sequence Database | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. HIV Sequence Database is a database of annotated HIV sequences, plus a variety of tools and information for researchers studying HIV and SIV. The main aim of this website is to provide easy access to our sequence database, alignments, and the tools and interfaces we have produced. The HIV Sequence Database focuses on five primary goals: * Collecting HIV and SIV sequence data (all sequences since 1987) * Curating and annotating this data, and making it available to the scientific community * Computer analysis of HIV and related sequences * Production of software for the analysis of (sequence) data * The data and analyses on this site and published in a yearly printed publication, the HIV sequence Compendium, which is available free of charge. | drug resistance, genetics, mutation, vaccine, human immunodeficiency virus, siv, sequence, alignment, simian immunodeficiency virus, FASEB list | has parent organization: HIV Databases | Human immunodeficiency virus, Simian immunodeficiency virus | NIAID | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02967 | SCR_002906 | 2026-02-13 10:55:08 | 108 | ||||||
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Weighted Gene Co-expression Network Analysis Resource Report Resource Website 1000+ mentions |
Weighted Gene Co-expression Network Analysis (RRID:SCR_003302) | WGCNA | data analysis software, software resource, data processing software, software application | Software R package for weighted correlation network analysis. WGCNA is also available as point-and-click application. Unfortunately this application is not maintained anymore. It is known to have compatibility problems with R-2.8.x and newer, and the methods it implements are not all state of the art., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, co-expression, analysis, network, bio.tools, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of California at Los Angeles; California; USA |
NCI P50CA092131; NIDA 1R01DA030913-01; NIDCR R01DE019255; NIAID U19 AI063603-01 |
PMID:19114008 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31889, biotools:crosslinkwgcna | http://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/Rpackages/WGCNA/#citation https://bio.tools/crosslinkwgcna |
SCR_003302 | WGCNA: an R package for weighted correlation network analysis | 2026-02-13 10:55:13 | 1860 | ||||
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Human Immunology Project Consortium Resource Report Resource Website 10+ mentions |
Human Immunology Project Consortium (RRID:SCR_001491) | HIPC | data or information resource, organization portal, portal, consortium | Consortium established to capitalize on recent advances in immune profiling methods in order to create a novel public resource that characterizes diverse states of the human immune system following infection; prior to and following vaccination against an infectious disease; or prior to and following treatment with an immune adjuvant that targets a known innate immune receptor(s). Through this program, well-characterized human cohorts are studied using a variety of modern analytic tools, including multiplex transcriptional, cytokine, and proteomic assays; multiparameter phenotyping of leukocyte subsets; assessment of leukocyte functional status; and multiple computational methods. Centralized research resources and a comprehensive, centralized database will be constructed for use by the greater scientific community. The information gained from the program will provide a comprehensive understanding of the human immune system and its regulation, and will reveal novel associations between components of the immune system and other biological systems, identify novel immune mediators and pathways, establish predictors of vaccine safety in different populations, and enable the rapid evaluation of different vaccine formulations and administration regimens in human populations. | immune profiling, immune system, infection, vaccine, infectious disease, immune adjuvant, immune receptor, multiplex assay, phenotyping, systems biology, mass spectrometry, regulation, mediator, pathway, database, leukocyte, transcriptome, proteome | is parent organization of: ImmuneSpace | Infection, Vaccination, Treatment with immune adjuvant | NIAID | Free, Freely available | SciRes_000173 | SCR_001491 | immune profiling, immuneprofiling.org | 2026-02-13 10:54:52 | 17 | |||||
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DAVID Resource Report Resource Website 10000+ mentions |
DAVID (RRID:SCR_001881) | DAVID | web service, data or information resource, data access protocol, software resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. Bioinformatics resource system including web server and web service for functional annotation and enrichment analyses of gene lists. Consists of comprehensive knowledgebase and set of functional analysis tools. Includes gene centered database integrating heterogeneous gene annotation resources to facilitate high throughput gene functional analysis. | functional domain, annotation, motif, protein, ontology enrichment, gene, high-throughput, functional classification, functional annotation, clustering, genome, pathway, gene-disease association, interaction, functional domain, motif, visualization, FASEB list |
is listed by: OMICtools is listed by: 3DVC is listed by: LabWorm is listed by: SoftCite is related to: Gene Ontology is related to: BioCarta Pathways is related to: KEGG has parent organization: NCI-Frederick |
NIAID NO1-CO-56000; NCI |
PMID:19131956 PMID:12734009 PMID:35325185 PMID:22543366 PMID:17980028 PMID:17576678 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30408, nif-0000-10451, OMICS_02220, SCR_003033 | http://david.abcc.ncifcrf.gov/ | SCR_001881 | DAVID Bioinformatics Resources, Visualization and Integrated Discovery Bioinformatics Resources, Database for Annotation Visualization and Integrated Discovery, The Database for Annotation, The Database for Annotation Visualization and Integrated Discovery Bioinformatics Resources | 2026-02-13 10:54:56 | 18488 | ||||
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The Immunology Database and Analysis Portal (ImmPort) Resource Report Resource Website 500+ mentions |
The Immunology Database and Analysis Portal (ImmPort) (RRID:SCR_012804) | ImmPort | ontology, data repository, storage service resource, portal, data or information resource, service resource, controlled vocabulary, disease-related portal, topical portal, database | Data sharing repository of clinical trials, associated mechanistic studies, and other basic and applied immunology research programs. Platform to store, analyze, and exchange datasets for immune mediated diseases. Data supplied by NIAID/DAIT funded investigators and genomic, proteomic, and other data relevant to research of these programs extracted from public databases. Provides data analysis tools and immunology focused ontology to advance research in basic and clinical immunology. | immunology, basic, clinical, data, share, store, analyze, exchange, dataset, immune, mediated, disease, analysis, tool, FASEB list |
is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: NIDDK Research Resources is affiliated with: Cytokine Registry is related to: MetaCyto is related to: The 10000 Immunomes is related to: NIAID |
Immune mediated disease | NIH ; NIAID ; DAIT ; NIAID HHSN266200400076C; NIAID HHSN272201200028C |
PMID:24791905 | nlx_152691 | http://www.immport.org/immport-open/public/home/home http://www.immport.org/ |
http://www.immport.org | SCR_012804 | Immunology Data and Analysis Portal, ImmPort system, ImmPort, Immunology Database and Analysis Portal | 2026-02-13 10:57:01 | 987 | |||
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NIH-CIDI Segmentation of PET Images based on Affinity Propagation Clustering Resource Report Resource Website 1+ mentions |
NIH-CIDI Segmentation of PET Images based on Affinity Propagation Clustering (RRID:SCR_014151) | data processing software, software application, segmentation software, software resource, image analysis software | A MATLAB GUI for segmenting and quantifying PET images with multi-focal and diffuse uptakes. It imports a PET image and allows the user to draw region of interests (ROIs) in 2D or 3D to roughly separate the object of interest from the background. The areas are then segmented using a PET image segmentation method based on Affinity Propagation clustering to cluster the image intensities into meaningful groups. For quantification, the Standardized Uptake Value measurements of the binary or the user defined ROI are SUVmax, SUVmean, and Volume (mm^3) and can be exported into an excel sheet. | matlab gui, pet image, region of interest, 2d, 3d, segmentation, affinity propagation clustering | Howard Hughes Medical Institute ; Center for Infectious Disease Imaging ; NIAID Intramural research program ; NIBIB ; NIH Directors New Innovator Award OD006492; NIAD R01AI079590; NIAID R01A1035272 |
Available to the research community | http://www.nitrc.org/projects/ap_seg_2013_nih | SCR_014151 | 2026-02-13 10:57:13 | 1 | |||||||||
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Tracer Resource Report Resource Website 1000+ mentions |
Tracer (RRID:SCR_019121) | data visualization software, data processing software, data analysis software, software application, software resource | Open source software tool for analysing trace files generated by Bayesian MCMC runs. Software package for visualising and analysing MCMC trace files generated through Bayesian phylogenetic inference. Provides kernel density estimation, multivariate visualisation, demographic trajectory reconstruction, conditional posterior distribution summary and more. | Analysing trace files, files generated by Bayesian MCMC runs, MCMC trace files, conditional posterior distribution summary, demographic trajectory reconstruction, Bayesian phylogenetic inference, kernel density estimation, multivariate visualisation | Wellcome Trust ; European Union Seventh Framework Programme ; NSF DMS 1264153; NIAID R01 AI107034; NIAID U19 AI135995 |
PMID:29718447 | Free, Available for download, Freely available | https://github.com/beast-dev/tracer http://gensoft.pasteur.fr/docs/Tracer/v1.6 http://beast.community/tracer https://github.com/beast-dev/tracer/releases/tag/v1.7.1 |
SCR_019121 | Tracer v1.7.1, Tracer v1.6 | 2026-02-13 10:58:21 | 1582 | |||||||
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ArchR Resource Report Resource Website 100+ mentions |
ArchR (RRID:SCR_020982) | data processing software, data analysis software, software toolkit, software application, software resource | Software R package for processing and analyzing single-cell ATAC-seq data. Used for integrative single cell chromatin accessibility analysis.Provides intuitive, user focused interface for complex single cell analysis, including doublet removal, single cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing. | single-cell ATAC-seq data analysis, single-cell ATAC-seq data processing, single cell chromatin accessibility analysis, doublet removal, single cell clustering, cell type identification, unified peak set generation, cellular trajectory identification, transcription factor footprinting | NHGRI RM1 HG007735; NHGRI UM1 HG009442; NCI R35 CA209919; NHGRI UM1 HG009436; NCI U2C CA233311; NIAID U19 AI057266; NIA K99 AG059918; American Society of Hematology Scholar Award ; International Collaborative Award ; Defense Advanced Research Project Agency ; Ray and Dagmar Dolby Family Fund ; Stanford Cancer Institute-Goldman Sachs Foundation Cancer Research Award |
PMID:33633365 | Free, Available for download, Freely available | https://github.com/GreenleafLab/ArchR https://www.archrproject.com/ https://github.com/GreenleafLab/ArchR_2020 |
SCR_020982 | 2026-02-13 10:58:26 | 358 | ||||||||
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DatA Tag Suite Resource Report Resource Website |
DatA Tag Suite (RRID:SCR_019236) | DATS | data or information resource, software toolkit, software resource, narrative resource, standard specification | Software suite to enable discoverability of datasets. Enables submission of metadata on datasets to DataMed. Has core set of elements, which are generic and applicable to any type of dataset, and extended set that can accommodate more specialized data types. Platform independent model developed by NIH BD2K bioCADDIE project for DataMed Data Discovery Index prototype being developed. Also available as annotated serialization in schema.org, which in turn is widely used by major search engines like Google, Microsoft, Yahoo and Yandex. | Data processing, data discovery, metadata submission, DataMed, data, discovery | NIAID U24 AI117966; ELIXIR EXCELERATE ; ELIXIR-UK |
PMID:28585923 | Free, Freely available | SCR_019236 | 2026-02-13 10:58:23 | 0 |
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