Searching the RRID Resource Information Network
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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SpiecEasi Resource Report Resource Website 10+ mentions |
SpiecEasi (RRID:SCR_022712) | SpiecEasi | software resource, software application, data analysis software, data processing software | Software R package for microbiome network analysis. Used for inference of microbial ecological networks from amplicon sequencing datasets. Combines data transformations developed for compositional data analysis with graphical model inference framework that assumes underlying ecological association network is sparse. | microbiome network analysis, amplicon sequencing datasets, microbial ecological networks inference | NIAID AI007180; NIDDK DK103358; NIGMS GM63270; Simons Foundation |
PMID:25950956 | Free, Available for download, Freely available | SCR_022712 | SParse InversE Covariance Estimation for Ecological Association Inference | 2026-02-12 09:47:43 | 15 | |||||||
|
outbreak.info Resource Report Resource Website 100+ mentions |
outbreak.info (RRID:SCR_018282) | data or information resource, portal, topical portal | Resource to aggregate all outbreak information into single location during outbreaks of emerging diseases, such as COVID-19. | COVID-19 data collection, single location, outbreak information, emerging disease |
is listed by: Data and Computational Resources to Address COVID-19 has parent organization: Scripps Research Institute |
COVID-19 | NIAID | Free, Freely available | SCR_018282 | 2026-02-12 09:46:49 | 113 | ||||||||
|
Database of Immune Cell Epigenomes Resource Report Resource Website 50+ mentions |
Database of Immune Cell Epigenomes (RRID:SCR_018259) | DICE | data access protocol, software resource, web service, database, data or information resource | Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics. Collection of identified cis-eQTLs for 12,254 unique genes, which represent 61% of all protein-coding genes expressed in human cell types. Datasets to help reveal effects of disease risk associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis. | Data set, immune cell expression, expression quantitative trait loci, epigenomics, data, cis-eQLC, gene, protein coding gene, human cell type, genetic polymorphism disease, immune cell, pathogenesis | has parent organization: La Jolla Institute for Immunology | William K. Bowes Jr Foundation ; NIAID R24 AI108564; NCRR S10 RR027366; NIH Office of the Director S10 OD016262 |
PMID:30449622 | Free, Freely available | SCR_018259 | Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics | 2026-02-12 09:47:01 | 59 | ||||||
|
TimeZone Resource Report Resource Website 1+ mentions |
TimeZone (RRID:SCR_018564) | software resource, software application, data analysis software, data processing software | Software package to detect footprints of positive selection for functionally adaptive point mutations in microbial genomes. | Detect footprint, positive selection, functionally adaptive, point mutation, microbial genome | NIGMS R01 GM084318; NIAID RC4 AI092828 |
PMID:23471110 | Free, Available for download, Freely available | SCR_018564 | 2026-02-12 09:46:53 | 1 | |||||||||
|
EpiModel Resource Report Resource Website 1+ mentions |
EpiModel (RRID:SCR_018539) | software toolkit, software resource, software application, data analysis software, data processing software | Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics. | Infectious disease, mathematical modeling, simulation, analysis, infectious disease dynamic, bio.tools |
is listed by: Debian is listed by: bio.tools |
NICHD R01 HD068395; NIMH R21 MH112449; NICHD R21 HD075662; NIDA P30 DA027828; NIAID P30 AI050409; NIAID P30 AI027757; NICHD T32 HD007543 |
PMID:29731699 | Free, Available for download, Freely available | biotools:epimodel | https://bio.tools/epimodel | SCR_018539 | 2026-02-12 09:46:53 | 7 | ||||||
|
GOnet Resource Report Resource Website 1+ mentions |
GOnet (RRID:SCR_018977) | analysis service resource, software resource, data access protocol, service resource, web service, production service resource | Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists. | Gene Ontology, interactive analysis, data, gene, protein, gene list, protein list, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools works with: Gene Ontology |
NIH Common Fund ; NIGMS ; NHGRI R24 HG010032; NIAID U19 AI118610; NIAID U19 AI118626 |
PMID:30526489 | biotools:GOnet | https://github.com/mikpom/gonet https://bio.tools/GOnet |
SCR_018977 | 2026-02-12 09:47:07 | 3 | |||||||
|
immuneXpresso Resource Report Resource Website |
immuneXpresso (RRID:SCR_017578) | text-mining software, software resource, service resource, software application, data or information resource | Software tool as text-mining engine that structures and standardizes knowledge of immune intercellular communication. Knowledgebase contains interactions and separate mentions of cells or cytokines in context of thousands of diseases. Intercellular interactions were text-mined from all available PubMed abstracts across disease conditions. | Structure, standardize, immune, cellular, interaction, cytokine, disease, cell, PubMed, abstract |
is listed by: NIDDK Information Network (dkNET) is listed by: OMICtools |
NIH ; NIAID ; Rappaport Family Institute for Research in the Medical Sciences |
PMID:29912209 | Free, Freely available | SCR_017578 | 2026-02-12 09:46:54 | 0 | ||||||||
|
MaAsLin2 Resource Report Resource Website 100+ mentions |
MaAsLin2 (RRID:SCR_023241) | software toolkit, software resource | SoftwareR package that identifies microbial taxa correlated with factors of interest using generalized linear models and mixed models.Used for efficiently determining multivariable association between clinical metadata and microbial meta'omic features. | Microbiome Multivariable Associations with Linear Models, | NSF DEB-2028280; NIAID U19AI110820; NHGRI R01HG005220; NIDDK R24DK110499; NIDDK U54DK102557 |
DOI:10.1371/journal.pcbi.1009442 | Free, Available for download, Freely available | https://huttenhower.sph.harvard.edu/maaslin/ | SCR_023241 | 2026-02-12 09:47:54 | 170 | ||||||||
|
ColabFold Resource Report Resource Website 100+ mentions |
ColabFold (RRID:SCR_025453) | source code, software resource | Software application offers accelerated prediction of protein structures and complexes by combining homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. Used for protein folding. | prediction of protein structures and complexes, protein folding, protein structure prediction, | Max Planck Society ; University of Göttingen ; National Research Foundation of Korea ; Seoul National University ; NIH Office of the Director DP5OD026389; NIAID R21AI156595; NSF |
PMID:35637307 | Free, Available for download, Freely available | https://github.com/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb | SCR_025453 | 2026-02-12 09:48:24 | 391 | ||||||||
|
ClipKIT Resource Report Resource Website 10+ mentions |
ClipKIT (RRID:SCR_026411) | source code, software application, software resource | Software fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes others. Multiple sequence alignment-trimming algorithm for accurate phylogenomic inference. | multiple sequence, alignment trimming, accurate phylogenomic inference, | Howard Hughes Medical Institute ; National Science Foundation ; Guggenheim Foundation ; Burroughs Wellcome Fund ; NIAID 1R56AI146096; Zhejiang University ; Fundamental Research Funds for the Central Universities |
PMID:33264284 | Free, Available for download, Freely available | SCR_026411 | 2026-02-12 09:48:23 | 35 | |||||||||
|
Xenopus laevis Research Resource for Immunobiology (XLRR) Resource Report Resource Website 1+ mentions |
Xenopus laevis Research Resource for Immunobiology (XLRR) (RRID:SCR_014354) | XLRR | material resource, biomaterial supply resource | A comprehensive resource specializing in the use of the amphibian Xenopus laevis (the African clawed frog) for biomedical and immunological research. Several genetically-defined inbred strains and clones are available for study. The facility also maintains and develops research tools such as transgenic animals, monoclonal antibodies, cell lines, DNA libraries, and molecular probes. XLRR includes a satellite facility devoted to study infectious diseases caused by iridovirus. Technical assistance, education, and training are also provided. | Immunology, cancer, inbred frog, cloned frog, monoclonal antibody, xenopus laevis, lymphoid tumor cell lines | NIAID | SCR_014354 | Xenopus laevis Research Resource, Xenopus laevis Research Resource for Immunobiology | 2026-02-12 09:45:52 | 4 | |||||||||
|
ReBATE Resource Report Resource Website |
ReBATE (RRID:SCR_017139) | software toolkit, software resource | Open source software Python package to compare relief based feature selection algorithms used in data mining. Used for feature selection in any bioinformatics problem with potentially predictive features and target outcome variable, to detect feature interactions without examination of all feature combinations, to detect features involved in heterogeneous patterns of association such as genetic heterogeneity . | compare, relief, feature, algorithm, data, mining, variable, heterogeneous, pattern, genetic | has parent organization: University of Pennsylvania; Philadelphia; USA | NIAID AI116794; NIDDK DK112217; NIEHS ES013508; NEI EY022300; NHLBI HL134015; NLM LM009012; NLM LM010098; NLM LM011360; NCATS TR001263; Warren Center for Network and Data Science |
PMID:30030120 | Free, Available for download, Freely available | https://epistasislab.github.io/ReBATE/ | SCR_017139 | Relief Based Algorithm Training Environment | 2026-02-12 09:47:02 | 0 | ||||||
|
New York University School of Medicine IonLab Core Facility Resource Report Resource Website 1+ mentions |
New York University School of Medicine IonLab Core Facility (RRID:SCR_021754) | service resource, access service resource, core facility | Electrophysiology core facility that is part of Ion Channels and Transporters in Immunity Research Program.Research area includes ion channel and transporter function and ionic signaling in immune cells.Users who are studying other cell types or organ systems are welcome.Provides assistance with experimental design, training, implementation, and data analysis. | USEDit, ABRF, ion channel, transporter function, ionic signaling, immune cells |
is listed by: ABRF CoreMarketplace has parent organization: New York University School of Medicine; New York; USA |
NIAID AI097302 | open | ABRF_1221 | https://coremarketplace.org/?FacilityID=1221 | SCR_021754 | IonLab | 2026-02-12 09:47:52 | 8 | ||||||
|
Pathogens Portal Node Toolbox Resource Report Resource Website |
Pathogens Portal Node Toolbox (RRID:SCR_027086) | software toolkit, software resource, source code | Software package and code for Pathogen Portal node (i.e. a local Pathogens Portal, such as the Swedish and Dutch Pathogens Portals). Allows users to create their own node quickly and easily. | Pathogen Portal node, Swedish Pathogens Portal, Dutch Pathogens Portal, SciLifeLab | NIAID U24AI183840 | Free, Available for download, Freely available | SCR_027086 | 2026-02-12 09:48:31 | 0 | ||||||||||
|
InterProSurf Resource Report Resource Website |
InterProSurf (RRID:SCR_027791) | software resource, web service, web application, data access protocol | Web server for predicting interacting sites on protein surfaces. Analyzes solvent-accessible residues likely to participate in PPIs.Predicts interacting amino acid residues in proteins that are most likely to interact with other proteins, given the 3D structures of subunits of protein complex. | Analyzes solvent-accessible residues, predicting interacting sites on protein surfaces, interacting amino acid residues in proteins, proteins that are most likely to interact with other proteins, | NIAID R21 AI055746; NIAID R01 AI064913 |
PMID:17933856 | Free, Freely available, | SCR_027791 | 2026-02-12 09:48:58 | 0 | |||||||||
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Cryptococcus Neoformans cDNA Sequencing Resource Report Resource Website 1+ mentions |
Cryptococcus Neoformans cDNA Sequencing (RRID:SCR_008462) | software resource | Cryptococcus neoformans is an encapsulated yeast that infects the human host via the respiratory tract where it usually causes an inapparent infection. In the susceptible host, it may disseminate, typically producing a chronic and life-threatening meningitis. The Cryptococcus neoformans serotypes A and D are responsible for the overwhelming majority of pulmonary infections in AIDS patients. Cryptococcus neoformans strain H99 Latest Data Release - May 19, 2004 To date, we have isolated ca. 3750 cDNA clones from Cryptococcus neoformans strain H99 in collaboration with Drs. Juneann Murphy and Dave Dyer at the University of Oklahoma Health Sciences Center''s Department of Microbiology and Immunology in Oklahoma City and Kent Buchanan at the Tulane University Medical School, New Orleans, LA. The Cryptococcus neoformans strain H99 EST''s have been generated by Doris Kupfer, Heather Bell, Sunkyoung So, Yuong Tang, and Jennifer Lewis at the University of Oklahoma''s Advanced Center for Genome Technology, in the Department of Chemistry and Biochemistry. We now have end sequenced all available templates (ca. 7500 reactions) from both ends of the directionally cloned inserts after excision into pBlueScript SK-. . All of our data is available from our ftp site, and we now have added the ability to perform blast searches on this data. A keyword search of a blastx search of GenBank with this data also is available but we have not yet linked this to a unigene database as the number of EST''s sequenced doesn''t warrent this yet. | has parent organization: University of Oklahoma; Oklahoma; USA | NIAID AI147079 | nif-0000-30397 | SCR_008462 | cDNA Sequencing | 2026-02-07 02:07:50 | 1 | |||||||||
|
MS-GF+ Resource Report Resource Website 100+ mentions |
MS-GF+ (RRID:SCR_015646) | software resource | Software that performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database. | protein idenitification, peptide sequence, ms, ms spectrum, proteomic, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: Pacific Northwest National Laboratory |
NCRR RR018522; NCRR 1-P41-RR024851; NIAID ; W.R. Wiley Environmental Molecular Science Laboratory |
PMID:25358478 | Free, Available for download, Acknowledgment requested | biotools:ms-gf | https://github.com/sangtaekim/msgfplus https://bio.tools/ms-gf |
SCR_015646 | MSGF+, MSGFPlus | 2026-02-07 02:09:19 | 151 | |||||
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IBEX Knowledge Base Resource Report Resource Website 1+ mentions |
IBEX Knowledge Base (RRID:SCR_025296) | knowledge base | Open, global repository as central resource for reagents, protocols, panels, publications, software, and datasets. In addition to IBEX, we support standard, single cycle multiplexed imaging (Multiplexed 2D imaging), volume imaging of cleared tissues with clearing enhanced 3D (Ce3D), highly multiplexed 3D imaging (Ce3D-IBEX), and extension of the IBEX dye inactivation protocol to the Leica Cell DIVE (Cell DIVE-IBEX). Committed to sharing knowledge related to multiplexed imaging. Antibody validation community knowledgebase. | Antibody, validation, multiplexed imaging, | NCI ; NIAID ; Schroeder Allergy and Immunology Research Institute ; McMaster University ; CA ; Chan Zuckerberg Initiative ; Wellcome Trust |
Free, Freely available | https://zenodo.org/records/7693279 | SCR_025296 | Iterative Bleaching Extends Multiplexity (IBEX) Knowledge-Base | 2026-02-07 02:16:47 | 3 | ||||||||
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ApiDB CryptoDB Resource Report Resource Website 10+ mentions |
ApiDB CryptoDB (RRID:SCR_013455) | ApiDB CryptoDB | data or information resource, database | 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 | https://bio.tools/cryptodb | http://cryptodb.org/ | SCR_013455 | CryptoDB, Cryptosporidium Genomics Resource | 2026-02-11 10:58:45 | 25 | ||||
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Cytokine Registry Resource Report Resource Website 1+ mentions |
Cytokine Registry (RRID:SCR_014368) | data or information resource, database | 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 | 2026-02-11 10:58:54 | 1 |
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