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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Phenograph Resource Report Resource Website 100+ mentions |
Phenograph (RRID:SCR_016919) | PhenoGraph | software application, data processing software, data analysis software, software resource | Software tool as clustering method designed for high dimensional single cell data. Algorithmically defines phenotypes in high dimensional single cell data. Used for large scale analysis of single cell heterogeneity. | high, dimention, single, cell, data, phenotype, analysis, heterogeneity |
uses: Python Programming Language is related to: Rphenograph |
NIGMS R00 GM104148; NICHD DP1 HD084071; NCI R01 CA164729; NCI U54 CA121852; NCI R01 CA130826; NCI U54 CA143907; US Department of Health and Human Services HHSN272200700038C; NIH N01 HV00242; NCI P01 CA034233; NIAID U19 AI057229; NCI U54 CA149145; US FDA HHSF223201210194C; US DOD W81XWH1210591; Entertainment Industry Foundation ; Rachford and Carlota Harris Endowed Professorship ; CIRM DR1 01477; CIRM RB201592; Stand Up To Cancer Phillip A. Sharp Award SU2CAACRPS04; Packard Fellowship for Science and Engineering ; NIH Office of the Director DP2 OD002414 |
PMID:26095251 | Free, Available for download, Freely available | https://github.com/JinmiaoChenLab/Rphenograph | https://github.com/jacoblevine/PhenoGraph | SCR_016919 | 2026-02-15 09:21:56 | 213 | |||||
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CheckMyMetal Resource Report Resource Website 1+ mentions |
CheckMyMetal (RRID:SCR_016887) | CMM | web service, data access protocol, software resource | Metal binding site validation server. Used for systematic inspection of the metal-binding architectures in macromolecular structures. The validation parameters that CMM examines cover the entire binding environment of the metal ion, including the position, charge and type of atoms and residues surrounding the metal. | metal, binging, site, validation, server, systematic, inspection, macromolecular, structure, ion, charge, position, atom | NIGMS GM117325; NHGRI HG008424; NIAID HHSN272201200026C |
PMID:28291757 | Free, Freely available | SCR_016887 | 2026-02-15 09:21:56 | 5 | ||||||||
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ImmuneDB Resource Report Resource Website 1+ mentions |
ImmuneDB (RRID:SCR_017125) | data analysis service, database, service resource, production service resource, data or information resource, analysis service resource | Software system for storing and analyzing high throughput B and T cell immune receptor sequencing data. Comprised of web interface and of Python analysis tools to process raw reads for gene usage, infer clones, aggregate data, and run downstream analyses, or in conjunction with other AIRR tools using its import and export features. | collect, store, analysis, B cell, T cell, immune, receptor, sequencing, data, process, raw, read | is used by: AIRR Data Commons | NIAID P01 AI106697; NIAID P30 AI0450080; NIDDK UC4 DK112217; NCI P30 CA016520 |
PMID:30298069 | Free, Available for download, Freely available | https://github.com/arosenfeld/immunedb | SCR_017125 | 2026-02-15 09:21:15 | 8 | |||||||
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immuneXpresso Resource Report Resource Website |
immuneXpresso (RRID:SCR_017578) | software application, software resource, service resource, text-mining software, 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 | 2026-02-15 09:22:09 | 0 | ||||||||
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Database of Immune Cell Epigenomes Resource Report Resource Website 50+ mentions |
Database of Immune Cell Epigenomes (RRID:SCR_018259) | DICE | database, software resource, data access protocol, web service, 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 | 2026-02-15 09:22:19 | 59 | ||||||
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Clinical Trials in Organ Transplantation (CTOT) Resource Report Resource Website 1+ mentions |
Clinical Trials in Organ Transplantation (CTOT) (RRID:SCR_015859) | CTOT | organization portal, portal, consortium, project portal, data or information resource | Project portal for a cooperative research program to improve short and long-term graft and patient survival. CTOT is an investigative consortium for conducting clinical and associated mechanistic studies that will lead to improved outcomes for transplant recipients. | graft, graft patient, patient survival, clinical study, transplant, transplant recipient, mechanistic study |
is listed by: NIDDK Information Network (dkNET) is listed by: Diabetes Research Centers is related to: Clinical Trials in Organ Transplantation in Children (CTOT-C) |
NIAID UM2 AI117870 | Public, Available to the scientific community | SCR_015859 | Clinical Trials in Organ Transplantation | 2026-02-15 09:21:40 | 1 | |||||||
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Clinical Trials in Organ Transplantation in Children (CTOT-C) Resource Report Resource Website 1+ mentions |
Clinical Trials in Organ Transplantation in Children (CTOT-C) (RRID:SCR_015860) | CTOT-C | organization portal, portal, consortium, project portal, data or information resource | Project portal for a cooperative research program sponsored by the National Institute of Allergy and Infectious Diseases (NIAID). CTOT-C is an investigative consortium for conducting clinical and associated mechanistic studies that will lead to improved outcomes for pediatric heart, lung, or kidney transplant recipients. | heart, kidney, lung, pediatric, cooperative research program, niaid, clinical study, mechanistic study, transplant |
is listed by: NIDDK Information Network (dkNET) is related to: Clinical Trials in Organ Transplantation (CTOT) |
NIAID UM2 AI117870 | Public, Available to the scientific community | SCR_015860 | NIAID Clinical Trials in Organ Transplantation in Children, Clinical Trials in Organ Transplantation in Children, NIAID CTOT-C | 2026-02-15 09:20:58 | 1 | |||||||
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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 | 2026-02-15 09:20:43 | 4 | |||||||||
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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 | 2026-02-15 09:21:57 | 0 | ||||||
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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 | 2026-02-15 09:23:06 | 170 | ||||||||
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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) | access service resource, core facility, service resource | 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 | 2026-02-15 09:22:09 | 8 | ||||||
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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 | 2026-02-15 09:23:00 | 391 | ||||||||
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ClipKIT Resource Report Resource Website 10+ mentions |
ClipKIT (RRID:SCR_026411) | software application, source code, 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 | 2026-02-15 09:23:16 | 35 | |||||||||
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Pathogens Portal Node Toolbox Resource Report Resource Website |
Pathogens Portal Node Toolbox (RRID:SCR_027086) | source code, software toolkit, software resource | 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 | 2026-02-15 09:23:30 | 0 | ||||||||||
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InterProSurf Resource Report Resource Website |
InterProSurf (RRID:SCR_027791) | web service, data access protocol, web application, software resource | 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 | 2026-02-15 09:24:17 | 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 | 2026-02-14 02:01:34 | 1 | |||||||||
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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 | 2026-02-14 02:01:57 | 0 | ||||||||
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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 | 2026-02-14 02:03:07 | 155 | |||||
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Sequencing of Idd regions in the NOD mouse genome Resource Report Resource Website 1+ mentions |
Sequencing of Idd regions in the NOD mouse genome (RRID:SCR_001483) | Sequencing of Idd regions in the NOD mouse genome | data or information resource, data set, resource | Genetic variations associated with type 1 diabetes identified by sequencing regions of the non-obese diabetic (NOD) mouse genome and comparing them with the same areas of a diabetes-resistant C57BL/6J reference mouse allowing identification of single nucleotide polymorphisms (SNPs) or other genomic variations putatively associated with diabetes in mice. Finished clones from the targeted insulin-dependent diabetes (Idd) candidate regions are displayed in the NOD clone sequence section of the website, where they can be downloaded either as individual clone sequences or larger contigs that make up the accession golden path (AGP). All sequences are publicly available via the International Nucleotide Sequence Database Collaboration. Two NOD mouse BAC libraries were constructed and the BAC ends sequenced. Clones from the DIL NOD BAC library constructed by RIKEN Genomic Sciences Centre (Japan) in conjunction with the Diabetes and Inflammation Laboratory (DIL) (University of Cambridge) from the NOD/MrkTac mouse strain are designated DIL. Clones from the CHORI-29 NOD BAC library constructed by Pieter de Jong (Children's Hospital, Oakland, California, USA) from the NOD/ShiLtJ mouse strain are designated CHORI-29. All NOD mouse BAC end-sequences have been submitted to the International Nucleotide Sequence Database Consortium (INSDC), deposited in the NCBI trace archive. They have generated a clone map from these two libraries by mapping the BAC end-sequences to the latest assembly of the C57BL/6J mouse reference genome sequence. These BAC end-sequence alignments can then be visualized in the Ensembl mouse genome browser where the alignments of both NOD BAC libraries can be accessed through the Distributed Annotation System (DAS). The Mouse Genomes Project has used the Illumina platform to sequence the entire NOD/ShiLtJ genome and this should help to position unaligned BAC end-sequences to novel non-reference regions of the NOD genome. Further information about the BAC end-sequences, such as their alignment, variation data and Ensembl gene coverage, can be obtained from the NOD mouse ftp site. | genome, sequencing, genome sequencing, insulin-dependent diabetes, c57bl/6j, single nucleotide polymorphism, genetic variation, bacterial artificial chromosome, sequence, gene, animal model, clone, annotation, contig |
lists: VEGA is listed by: NIDDK Information Network (dkNET) has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Type 1 diabetes, Diabetes | NIAID AI 15416; NIDDK ; JDRF |
PMID:23729657 | Free, Freely available | nlx_152738 | http://www.sanger.ac.uk/resources/mouse/nod/ | SCR_001483 | Sequencing of Insulin-dependent diabetes regions in the NOD mouse genome | 2026-02-14 02:05:20 | 1 | |||
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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 | 2026-02-14 02:06:03 | 37 |
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