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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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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 | database, data or information resource | 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 | 2026-08-04 09:41:51 | 37 | |||||
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CRCView Resource Report Resource Website |
CRCView (RRID:SCR_007092) | CRCView | data analysis service, analysis service resource, production service resource, service resource | Web-based microarray data analysis and visualization system powered by CRC, or Chinese Restaurant cluster, a Dirichlet process model-based clustering algorithm recently developed by Dr. Steve Qin. It also incorporates several gene expression analysis programs from Bioconductor, including GOStats, genefilter, and Heatplus. CRCView also installs from the Bioconductor system 78 annotation libraries of microarray chips for human (31), mouse (24), rat (14), zebrafish (1), chicken (1), Drosophila (3), Arabidopsis (2), Caenorhabditis elegans (1), and Xenopus Laevis (1). CRCView allows flexible input data format, automated model-based CRC clustering analysis, rich graphical illustration, and integrated Gene Ontology (GO)-based gene enrichment for efficient annotation and interpretation of clustering results. CRC has the following features comparing to other clustering tools: 1) able to infer number of clusters, 2) able to cluster genes displaying time-shifted and/or inverted correlations, 3) able to tolerate missing genotype data and 4) provide confidence measure for clusters generated. You need to register for an account in the system to store your data and analyses. The data and results can be visited again anytime you log in. | microarray, gene expression, cluster, gene, expression profile, data repository, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Bioconductor is related to: Gene Ontology has parent organization: University of Michigan; Ann Arbor; USA |
University of Michigan; Michigan; USA ; Institutional Fund ; NIH U013422; NIAID 1R21AI057875-01 |
PMID:17485426 | Registration required | biotools:crcview, nlx_99864 | https://bio.tools/crcview | http://helab.bioinformatics.med.umich.edu/crcview/ | SCR_007092 | Chinese Restaurant ClusterView | 2026-08-04 09:41:45 | 0 | |||
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ImmGen Resource Report Resource Website 100+ mentions |
ImmGen (RRID:SCR_021792) | database, data or information resource | 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 | 2026-08-04 09:44:55 | 258 | ||||||||
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ApiDB CryptoDB Resource Report Resource Website 10+ mentions |
ApiDB CryptoDB (RRID:SCR_013455) | ApiDB CryptoDB | database, data or information resource | An integrated genomic and functional genomic database for the parasite Cryptosporidium. CryptoDB integrates whole genome sequence and annotation along with experimental data and environmental isolate sequences provided by community researchers. The database includes supplemental bioinformatics analyses and a web interface for data-mining. Organisms included in CryptoDB are Cryptosporidium parvum, Cryptosporidium hominis, Cryptosporidium muris and environmental isolate sequences from numerous species. CryptoDB is allied with the databases PlasmoDB and ToxoDB via ApiDB, an NIH/NIAID-funded Bioinformatics Resource Center. Tools include: * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Cryptosporidium Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * CryptoCyc: Explore Automatically Defined Metabolic Pathways * Searches via Web Services: Web service access to our data | cryptosporidium parvum, cryptosporidium, cryptosporidium genome, cryptosporidium orf, cryptosporidium sage tag alignments, cryptosporidium snp, genomic sequence, dna motif, snp, est, orf, data set, bio.tools |
uses: SynView is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Eukaryotic Pathogen Database Resources |
NIAID contract HHSN266200400037C | PMID:16381902 | nif-0000-02698, biotools:cryptodb, r3d100012265 | https://bio.tools/cryptodb | http://cryptodb.org/ | SCR_013455 | CryptoDB, Cryptosporidium Genomics Resource | 2026-08-04 09:43:13 | 25 | ||||
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Cytokine Registry Resource Report Resource Website 1+ mentions |
Cytokine Registry (RRID:SCR_014368) | database, data or information resource | A registry of cytokines, chemokines, and receptors generated for the purpose of collecting, integrating, and mapping between entity names and synonyms from several resources. These resources include MeSH, the Protein Ontology, EntrezGene, HGNC, MGI, UniProt and others. | cytokine, registry, innate immune system, chemokine, receptor |
uses: UniProt uses: MeSH uses: Plant Ontology uses: Mouse Genome Informatics (MGI) uses: HGNC uses: Entrez Gene is affiliated with: The Immunology Database and Analysis Portal (ImmPort) has parent organization: University of California at San Francisco; California; USA |
NIAID ; NIH ; Department of Health and Human Services |
Acknowledgement required, Registry file is available for download | SCR_014368 | ImmPort Cytokine Registry | 2026-08-04 09:43:24 | 1 | ||||||||
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EPIMHC Resource Report Resource Website 1+ mentions |
EPIMHC (RRID:SCR_016279) | database, data or information resource | 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 | 2026-08-04 09:43:51 | 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 | database, data or information resource | 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 | 2026-08-04 09:43:56 | 42 | |||||||
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BEI Resource Repository Resource Report Resource Website 100+ mentions |
BEI Resource Repository (RRID:SCR_013698) | storage service resource, biobank, material storage repository, service resource | Central data repository that supplies organisms and reagents to the broad community of microbiology and infectious diseases researchers. | biomaterial, material, reagent, microbiology, infectious diseases |
is listed by: NIH Data Sharing Repositories is related to: ATCC is related to: NIH Data Sharing Repositories |
infectious disease | NIAID | SCR_013698 | BEI Resource | 2026-08-04 09:43:16 | 216 | ||||||||
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xCell Resource Report Resource Website 50+ mentions |
xCell (RRID:SCR_026446) | web application, software toolkit, software resource, source code | Software R package for generating cell type scores and R scripts for development of xCell. Web tool that performs cell type enrichment analysis from gene expression data for immune and stroma cell types. Used for Cell types enrichment analysis. | Cell types enrichment analysis, cell type, enrichment analysis, generating cell type scores and R scripts, development of xCell, | Gruss Lipper Postdoctoral Fellowship ; NCI U24 CA195858; NIAID |
PMID:29141660 | Free, Available for download, Freely available | http://xCell.ucsf.edu/ | SCR_026446 | 2026-08-04 09:45:59 | 62 | ||||||||
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chromvar Resource Report Resource Website 10+ mentions |
chromvar (RRID:SCR_026570) | data processing software, source code, data analysis software, software resource, software application, software toolkit | Software R package for analyzing sparse chromatin-accessibility data by estimating gain or loss of accessibility within peaks sharing the same motif or annotation while controlling for technical biases. Enables accurate clustering of scATAC-seq profiles and characterization of known and de novo sequence motifs associated with variation in chromatin accessibility. Used for analysis of sparse chromatin accessibility data from single cell or bulk ATAC or DNAse-seq data. | analyzing sparse chromatin-accessibility data, analysis of sparse chromatin accessibility data, single cell, bulk ATAC, DNAse-seq data, | is used by: pychromVAR | NHGRI P50HG007735; NIAID U19AI057266; Rita Allen Foundation ; Harvard Society of Fellows ; Broad Institute Fellowship |
PMID:28825706 | Free, Available for download, Freely available | SCR_026570 | chromatin Variability Across Regions | 2026-08-04 09:46:01 | 11 | |||||||
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CytoML Resource Report Resource Website 1+ mentions |
CytoML (RRID:SCR_027485) | software resource, software toolkit, source code | Software R package that enables cross-platform import, export, and sharing of gated cytometry data. It currently supports Cytobank, FlowJo, Diva, and R, allowing users to import gated cytometry data from commercial platforms into R. | Cross-platform cytometry data sharing, cross-platform import, export, sharing, gated cytometry data, import gated cytometry data, | NIGMS R01 GM118417; Bill and Melinda Gates Foundation ; NIAID UM1 AI068635 |
PMID:30551257 | Free, Available for download, Freely available | https://www.bioconductor.org/packages/release/bioc/html/CytoML.html | SCR_027485 | 2026-08-04 09:46:13 | 5 | ||||||||
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demuxlet Resource Report Resource Website |
demuxlet (RRID:SCR_027855) | software application, software resource, source code | Software tool that harnesses natural genetic variation to determine the sample identity of each droplet containing a single cell (singlet) and detect droplets containing two cells (doublets). Genetic multiplexing of barcoded single cell RNA-seq. | Genetic multiplexing of barcoded single cell RNA-seq, harnesses natural genetic variation, | NIAMSD R01AR071522; NIAID R21AI133337; NIDDK F30DK115167; NHLBI K25HL121295; NIDCR R03DE025665 |
PMID:29227470 | Free, Available for download, Freely available | SCR_027855 | 2026-08-04 09:46:18 | 0 | |||||||||
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EpiProfile Resource Report Resource Website |
EpiProfile (RRID:SCR_028224) | software application, software resource, source code | Software tool for processing Epi-Proteomics mass spectrometry data. Discriminates isobaric histone peptides using distinguishing fragment ions in their tandem mass spectra and extracts the chromatographic area under the curve using previous knowledge about peptide retention time. Nanoflow liquid chromatography coupled with high resolution tandem mass spectrometry-based quantification tool for histone peptides, which can also be adapted to analyze nonhistone protein samples. EpiProfile 2.0 is extended version of v1.0 for enhanced quantification of histone peptides based on LC-MS/MS analysis. | LC-MS/MS analysis, peptide, quantification, histone, quantification of histone peptides, quantification of histone peptides based on LC-MS/MS analysis, mass spectrometry data, | NIGMS GM110174; NIAID AI118891; NCI CA196539; UPenn Epigenetics Institute ; NCATS TL1TR001880; NIGMS T32GM008275 |
PMID:25805797 PMID:29790754 |
Free, Available for download, Freely available | SCR_028224 | EpiProfile 2.0 | 2026-08-04 09:46:22 | 0 | ||||||||
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starCAT Resource Report Resource Website |
starCAT (RRID:SCR_028475) | software resource, software toolkit, source code | Software pipeline that improves T cell characterization by simultaneously quantifying predefined gene expression programs (scRNA-Seq) capturing activation states and cellular subsets. Used to score cells based on a fixed, multidataset catalog of Gene Expression Programs from any tissues or cell-type. | T cell characterization, simultaneously quantifying predefined gene expression programs, gene expression programs, | NIAID P01AI148102; NHGRI U01HG012009; NIAMS R01AR063759; NHGRI R56HG013083; NHGRI T32HG002295; NIAMS T32AR007530 |
PMID:38746317 | Free, Available for download, Freely available | SCR_028475 | starCellAnnoTator, starCellAnnoTator (starCAT) | 2026-08-04 09:46:26 | 0 | ||||||||
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TryTripDB Resource Report Resource Website |
TryTripDB (RRID:SCR_028607) | database, data or information resource | Free online resource for data mining of genomic and functional data from these kinetoplastid parasites and is part of the VEuPathDB Bioinformatics Resource Center. Integrates functional genome scale datasets (e.g. transcript expression, protein expression, genetic variation data) and information predicted from automated bioinformatics pipelines and from manual curation. Provides a user friendly web interface and a number of tools and functions for users to conduct in silico experiments to ask questions and generate hypotheses. Researchers can also contribute their expertise via the User Comments form and Apollo annotation platform, and utilize cloud-based workspace to analyze their own data. | data mining, genomic data, functional data, kinetoplastid parasites, | NIAID ; Wellcome Trust |
PMID:36656904 | Free, Freely available | SCR_028607 | 2026-08-04 09:46:28 | 0 |
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