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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-07-25 12:08:11 | 155 | |||||
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CharProtDB: Characterized Protein Database Resource Report Resource Website |
CharProtDB: Characterized Protein Database (RRID:SCR_005872) | CharProtDB | database, data or information resource | 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 | 2026-07-25 12:11:41 | 0 | |||||
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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 | 2026-07-25 12:12:11 | 42 | |||||||
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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 | 2026-07-25 12:12:16 | 258 | ||||||||
|
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 | 2026-07-25 12:12:07 | 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 | 2026-07-25 12:12:09 | 1 | ||||||||
|
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 | 2026-07-25 12:12:12 | 4 | ||||||||
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Human Immunology Project Consortium Resource Report Resource Website 10+ mentions |
Human Immunology Project Consortium (RRID:SCR_001491) | HIPC | organization portal, consortium, portal, data or information resource | 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 | 2026-07-26 09:02:59 | 17 | |||||
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Tree-Based Pipeline Optimization Tool Resource Report Resource Website 1+ mentions |
Tree-Based Pipeline Optimization Tool (RRID:SCR_017531) | TPOT | software resource, software toolkit | Software Python package to automate building of ML pipelines by combining flexible expression tree representation of pipelines with stochastic search algorithms such as genetic programming. | Automated, machine, learning, optimize, pipeline, genetic, programming | NIAID R01 AI117694 | Free, Available for download, Freely available | SCR_017532 | https://epistasislab.github.io/tpot/, https://github.com/EpistasisLab/tpot | SCR_017531 | Tree based Pipeline Optimization Tool | 2026-07-25 12:13:05 | 1 | ||||||
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MassQL Resource Report Resource Website 1+ mentions |
MassQL (RRID:SCR_025106) | software resource, source code | Software application for universal searching of Mass Spectrometry data. Open source MS query language for flexible and mass spectrometer manufacturer-independent mining of MS data. Implements common MS terminology to build consensus vocabulary to search for MS patterns in single mass spectrometry run. Enables set of mass spectrometry patterns to be queried directly from raw data. | Mass Spectrometry data searching, mass spectrometry data, mining of MS data, common MS terminology, mass spectrometry patterns, raw data query, | NIGMS R01 GM125943; NIGMS R01 GM107550; NIGMS R35 GM128690; NIAID R21 AI156669; NIAID R15 AI137996; NSF ; Burroughs Wellcome Fund ; University of Michigan ; National Research Foundation of Korea ; German Research Foundation ; Swedish Research Council ; Ministry of Innovative Development of the Republic of Uzbekistan ; German Ministry for Education and Research ; Horizon 2020 programme of the European Union ; Czech Science Foundation ; U.S. Department of Energy Joint Genome Institute ; National Cancer Center Research and Development Fund ; AMED Japan Program for Infectious Diseases Research and Infrastructure ; Novo Nordisk Foundation ; Denmark ; Betty and Gordon Moore Foundation |
DOI:10.1101/2022.08.06.503000 | Free, Available for download, Freely available | https://pypi.org/project/massql/ | SCR_025106 | Mass Spec Query Language | 2026-07-25 12:14:51 | 1 | |||||||
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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 | 2026-07-25 12:14:56 | 3 | ||||||||
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Sparse Inverse Covariance Estimation for Ecological Association Inference Resource Report Resource Website 10+ mentions |
Sparse Inverse Covariance Estimation for Ecological Association Inference (RRID:SCR_022646) | SPIEC-EASI | software resource, software toolkit | Software R package estimates inverse covariance matrix from sequencing data.Statistical method for inference of microbial ecological networks from amplicon sequencing datasets. | inverse covariance matrix estimation, sequencing data, microbial ecological networks inference, amplicon sequencing datasets microbial ecological networks, | NIAID T32AI007180; NIDDK R01 DK103358; NIGMS RO1 GM63270; Simons Foundation |
PMID:25950956 | Free, Available for download, Freely available | SCR_022646 | SParse InversE Covariance Estimation for Ecological Association Inference | 2026-07-25 12:13:09 | 12 | |||||||
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SingleR Resource Report Resource Website 100+ mentions |
SingleR (RRID:SCR_023120) | software resource, software toolkit | Software R package for unbiased cell type recognition of scRNA-seq data. Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer cell of origin of each single cell independently. | unbiased cell type recognition, scRNA-seq data, reference transcriptomic datasets, pure cell types, infer cell of origin | UCSF Marcus Award ; NHLBI HL131560; UCSF Nina Ireland Program award ; NHLBI HL139897; NIAID |
PMID:30643263 | Free, Available for download, Freely available | https://github.com/dviraran/SingleR, https://github.com/LTLA/SingleR | SCR_023120 | Single-cell RNA-seq cell types Recognition | 2026-07-25 12:13:10 | 321 | |||||||
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DADA2 Resource Report Resource Website 500+ mentions |
DADA2 (RRID:SCR_023519) | software resource, software toolkit | Open source software R package for modeling and correcting Illumina sequenced amplicon errors. Fast and accurate sample inference from amplicon data with single nucleotide resolution. | modeling and correcting amplicon errors, Illumina sequenced amplicon errors, amplicon errors, sample inference, amplicon data, single nucleotide resolution |
is used by: ImmuMicrobiome is related to: dadasnake has parent organization: Stanford University; Stanford; California |
NSF ; NIAID R01AI112401; Samarth Foundation |
PMID:27214047 | Free, Available for download, Freely available | https://bioconductor.org/packages/dada2/ | SCR_023519 | 2026-07-25 12:13:12 | 960 | |||||||
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ATHLATES Resource Report Resource Website 1+ mentions |
ATHLATES (RRID:SCR_023689) | software resource, software toolkit | Software package for determining HLA genotypes for individuals from Illumina exome sequencing data. Program applies assembly, allele identification and allelic pair inference to short read sequences, and applies it to data from Illumina platforms. | Illumina, HLA genotypes determination, Illumina exome sequencing data, allele identification, allelic pair inference, short read sequence, | Washington University School of Medicine ; NIAID ; National Institutes of Health ; Department of Health and Human Services |
PMID:23748956 | Free, Available for download, Freely available | SCR_023689 | 2026-07-25 12:13:13 | 3 | |||||||||
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drug perturbation Gene Set Enrichment Analysis Resource Report Resource Website 1+ mentions |
drug perturbation Gene Set Enrichment Analysis (RRID:SCR_025351) | dpGSEA | software resource, source code | Software tool to detect phenotypically relevant drug targets through unique transcriptomic enrichment that emphasizes biological directionality of drug-derived gene sets. Exploratory tool to screen for possible drug targeting molecules. | detect phenotypically relevant drug targets, drug-derived gene sets, transcriptomic enrichment, | NHLBI T32HL007567; NIAID P30AI036219 |
DOI:10.1186/s12859-020-03929-0 | Free, Available for download, Freely available | SCR_025351 | 2026-07-25 12:14:57 | 1 | ||||||||
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Mixed effects association testing for single cells Resource Report Resource Website 1+ mentions |
Mixed effects association testing for single cells (RRID:SCR_025632) | MASC | software resource, source code | Software tool for testing whether specified covariate influences membership of single cells in any of multiple cellular subsets while accounting for technical confounds and biological variation. | specified covariate, influences membership, single cells, multiple cellular subsets, accounting for technical confounds and biological variation, | NIAMSD UH2AR067677; NIAID U19AI111224; NIAMSD 1R01AR063759; NIAMSD R01 AR064850; Doris Duke Charitable Foundation ; NIAMSD T32 AR007530; William Docken Inflammatory Autoimmune Disease Fund ; Ruth L. Kirschstein National Research Service Award ; Rheumatology Research Foundation Tobe and Stephen Malawista |
PMID:30333237 | SCR_025632 | , Mixed-effects modeling of Associations of Single Cells, Mixed-effects Association testing for Single Cells | 2026-07-25 12:15:05 | 2 | ||||||||
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Dynamic Regulatory Events Miner Resource Report Resource Website 1+ mentions |
Dynamic Regulatory Events Miner (RRID:SCR_003080) | DREM | software application, software resource, data processing software | The Dynamic Regulatory Events Miner (DREM) allows one to model, analyze, and visualize transcriptional gene regulation dynamics. The method of DREM takes as input time series gene expression data and static transcription factor-gene interaction data (e.g. ChIP-chip data), and produces as output a dynamic regulatory map. The dynamic regulatory map highlights major bifurcation events in the time series expression data and transcription factors potentially responsible for them. DREM 2.0 was released and supports a number of new features including: * new static binding data for mouse, human, D. melanogaster, A. thaliana * a new and more flexible implementation of the IOHMM supports dynamic binding data for each time point or as a mix of static/dynamic TF input * expression levels of TFs can be used to improve the models learned by DREM * the motif finder DECOD can be used in conjuction with DREM and help find DNA motifs for unannotated splits * new features for the visualization of expressed TFs, dragging boxes in the model view, and switching between representations | transcription, gene regulation, dynamics, time series, gene expression, static, dynamic, transcription factor-gene interaction, chip-chip, transcription factor, regulatory network, hidden markov model, systems biology, gene regulatory network, times series expression data, dynamic network, chip-seq | has parent organization: Carnegie Mellon University; Pennsylvania; USA | NIH ; NIGMS 1RO1 GM085022; NIAID DNO1 AI-5001; NSF 0448453 |
PMID:22897824 | Free, Available for download, Freely available | nif-0000-30478 | SCR_003080 | Dynamic Regulatory Events Miner (DREM) | 2026-07-26 09:03:21 | 5 | |||||
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Short Time-series Expression Miner (STEM) Resource Report Resource Website 50+ mentions |
Short Time-series Expression Miner (STEM) (RRID:SCR_005016) | STEM | software application, software resource, data processing software | The Short Time-series Expression Miner (STEM) is a Java program for clustering, comparing, and visualizing short time series gene expression data from microarray experiments (~8 time points or fewer). STEM allows researchers to identify significant temporal expression profiles and the genes associated with these profiles and to compare the behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology (GO) database supporting GO category gene enrichment analyses for sets of genes having the same temporal expression pattern. STEM also supports the ability to easily determine and visualize the behavior of genes belonging to a given GO category or user defined gene set, identifying which temporal expression profiles were enriched for these genes. (Note: While STEM is designed primarily to analyze data from short time course experiments it can be used to analyze data from any small set of experiments which can naturally be ordered sequentially including dose response experiments.) Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | statistical analysis, term enrichment, visualization, cluster, compare, short time series, gene expression, microarray, expression profile, gene, gene ontology, gene enrichment analyses, FASEB list |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Carnegie Mellon University; Pennsylvania; USA |
NIAID NO1 AI-5001; NSF 0448453 |
PMID:16597342 PMID:15961453 |
Open unspecified license - Free for academic use | nlx_97053 | SCR_005016 | Short Time-series Expression Miner | 2026-07-26 09:03:50 | 81 | |||||
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DICOMConvert Resource Report Resource Website |
DICOMConvert (RRID:SCR_014100) | software application, software resource, standalone software | A DICOM image converter based on the ITK IO mechanism for reading and writing images. The formats currently supported by the converter are DICOM to: Analyze (*.hdr); MetaImage (*.mhd); Nrrd (*.nhdr, *.nrrd). | standalone software, dicom, image converter |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National Institutes of Health |
Center for Infectious Disease Imaging ; NIAID ; NIBIB |
Available for download | SCR_014100 | Dicom Converter | 2026-07-26 09:06:02 | 0 |
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