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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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EASE: the Expression Analysis Systematic Explorer Resource Report Resource Website 50+ mentions |
EASE: the Expression Analysis Systematic Explorer (RRID:SCR_013361) | EASE | software resource, data processing software, software application | Windows(c) desktop software application, customizable and standalone, that facilitates the biological interpretation of gene lists derived from the results of microarray, proteomic, and SAGE experiments. Provides statistical methods for discovering enriched biological themes within gene lists, generates gene annotation tables, and enables automated linking to online analysis tools. Offers statistical models to deal with multi-test comparison problem. Platform: Windows compatible | gene, microarray, genome, gene ontology, statistical analysis, enrichment analysis, FASEB list |
is listed by: 3DVC is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Database for Annotation Visualization and Integrated Discovery |
NIAID | PMID:12734009 PMID:19131956 PMID:19033363 |
Free for academic use | nlx_149218 | SCR_013361 | Expression Analysis Systematic Explorer | 2026-02-14 02:05:32 | 94 | |||||
|
NS-Forest Resource Report Resource Website 1+ mentions |
NS-Forest (RRID:SCR_018348) | software resource, data processing software, software application | Software tool as method that takes cluster results from single cell nuclei RNAseq experiments and generates lists of minimal markers needed to define each cell type cluster. Utilizes random forest of decision trees machine learning approach. Used to determine minimum set of marker genes whose combined expression identified cells of given type with maximum classification accuracy. | Single cell, RNAseq experiment, generated gene list, minimum set, marker gene, define cell type cluster, random forest, decision tree, machine learning, identify cell, cell clasyfication | is related to: Allen Institute for Brain Science | Allen Institute for Brain Science ; JCVI Innovation Fund ; NIAID R21 AI122100; NIAID U19 AI118626; California Institute for Regenerative Medicine ; Wellcome Trust ; Chan Zuckerberg Initiative DAF |
PMID:29590361 | Free, Available for download, Freely available | SCR_018348 | Necessary and Sufficient Forest, NS-Forestversion 1.3, NS-Forest v2.0, NS-Forest version 1.0 | 2026-02-14 02:05:17 | 2 | |||||||
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proMODMatcher Resource Report Resource Website 1+ mentions |
proMODMatcher (RRID:SCR_017219) | data analysis software, software resource, data processing software, software application | Software tool as probabilistic multi omics data matching procedure to curate data, identify and correct data annotation and errors in large databases. Used to check potential labeling errors in profiles where number of cis relationships is small, such as miRNA and RPPA profiles. | probabilistic, matching, curate, omic, data, identify, correct, error, large, database, analysis, sample, label, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Icahn School of Medicine at Mount Sinai; New York; USA |
NHGRI U01 HG008451; NIA R01 AG046170; NIAID U19 AI118610 |
biotools:modmatcher | https://bio.tools/modmatcher | SCR_017219 | probabilisticMulti Omics DataMatcher | 2026-02-14 02:03:16 | 1 | |||||||
|
Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions Resource Report Resource Website |
Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions (RRID:SCR_017140) | HIBACHI, hibachi | software resource, simulation software, software application | Software tool that creates data sets with particular characteristics. Method and open source software for simulating complex biological and biomedical data to aid in comparing and evaluating machine learning methods. | data, simulation, dataset, compare, machine, evaluate, learning, method | NLM LM012601; NIAID AI116794; NIDDK DK112217 |
PMID:29218887 | Free, Available for download, Freely available | SCR_017140 | Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions | 2026-02-14 02:03:15 | 0 | |||||||
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Minimum Information about Biosynthetic Gene cluster Resource Report Resource Website 50+ mentions |
Minimum Information about Biosynthetic Gene cluster (RRID:SCR_023660) | MIBiG | data or information resource, portal, database, project portal | MIBiG is genomic standards consortium project and biosynthetic gene cluster database used as reference dataset. Provides community standard for annotations and metadata on biosynthetic gene clusters and their molecular products. Standardised data format that describes minimally required information to uniquely characterise biosynthetic gene clusters. MIBiG 2.0 is expended repository for biosynthetic gene clusters of known function. MIBiG 3.0 is database update comprising large scale validation and re-annotation of existing entries and new entries. Community driven effort to annotate experimentally validated biosynthetic gene clusters. | Genomic standards consortium project, community standard, annotations and metadata standards, biosynthetic gene clusters, sequence framework, biosynthetic gene cluster data, | Netherlands Organization for Scientific Research VENI grant ; NSF CAREER Award ; UK Biotechnology and Biological Sciences Research Council ; Novo Nordisk Foundation ; NIH U41 AT008718; Danish National Research Foundation ; NCCIH U24 AT010811; NCCIH F32 AT011475; Natural Sciences and Engineering Council of Canada Discovery grant ; European Union Horizon 2020 projects CARTNET ; Horizon 2020 Marie Skłodowska-Curie ; U.S. Department of Energy ; Portuguese Science and Technology Foundation ; U.S. National Science Foundation ; National Research Foundation of Korea ; NIGMS GM134688; NIAID R01AI155694; Netherlands eScience Center Accelerating Scientific Discoveries Grant ; Funds of the Chemical Industry Germany ; UK government Department for Environment ; Food and Rural Affairs ; German Chemical Industry ; Natural Sciences and Engineering Council of Canada |
PMID:36399496 DOI:10.1093/nar/gkz882 |
Free, Freely available | SCR_023660 | MIBiG 3.0, MIBiG 2.0 | 2026-02-14 02:05:38 | 55 | |||||||
|
DrInsight Resource Report Resource Website 1+ mentions |
DrInsight (RRID:SCR_023871) | data analysis software, software resource, data processing software, software application | Software connectivity mapping based drug repurposing tool that identifies drugs that can potentially reverse query disease phenotype or have similar functions with query drugs. | connectivity mapping based drug repurposing, identifies drugs, reverse query disease phenotype, query drugs, | NIAID U19AI082715 | PMID:30624606 | Free, Available for download, Freely available | https://github.com/cran/DrInsight | SCR_023871 | 2026-02-14 02:04:52 | 1 | ||||||||
|
celltrackR Resource Report Resource Website 1+ mentions |
celltrackR (RRID:SCR_021021) | data processing software, data analysis software, software toolkit, software application, software resource | Software R package to analyze immune cell migration data. Supports pipeline for track analysis by providing methods for data management, quality control, extracting and visualizing migration statistics, clustering tracks, and simulating cell migration.Available measures include displacement, confinement ratio, autocorrelation, straightness, turning angle, and fractal dimension. Measures can be applied to entire tracks, steps, or subtracks with varying length. | Immune cell migration data, dimensional space, cell analysis, cell migration, cell tracks, cell migration data, displacement, confinement ratio, autocorrelation, turning angle, fractal dimension | is listed by: CRAN | NIAID U01 AI095550; NIAID R01 AI077600 |
DOI:10.1101/670505v1 | Free, Available for download, Freely available | https://github.com/ingewortel/celltrackR | SCR_021021 | 2026-02-14 02:04:36 | 7 | |||||||
|
Differential Gene Correlation Analysis Resource Report Resource Website 1+ mentions |
Differential Gene Correlation Analysis (RRID:SCR_020964) | DGCA | data analysis software, software resource, data processing software, software application | Software R package to perform differential gene correlation analysis. Performs differential correlation analysis on input matrices, with multiple conditions specified by design matrix. | Differential gene, gene, gene correlation, correlation analysis, input matrices, differential correlations, identifier pairs, gene expression data, calculate differential correlations | is listed by: CRAN | NIA F30 AG052261; NIA R01 AG046170; NCI R01 CA163772; NIAID U01 AI111598 |
PMID:27846853 | Free, Available for download, Freely available | https://github.com/andymckenzie/DGCA | SCR_020964 | 2026-02-14 02:04:40 | 1 | ||||||
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nTracer Resource Report Resource Website |
nTracer (RRID:SCR_023032) | image processing software, software resource, data processing software, software application | Software tool as plug-in for ImageJ software. Used for tracing microscopic images. | tracing microscopic images | is a plug in for: ImageJ | Michigan miBRAIN initiative ; NIAID R01AI130303; NSF NSF-1707316; NIMH R01MH110932; NIGMS F31GM116517; NINDS R01NS095367; NIMH P50MH09427; NIH Office of the Director DP2OD006514; NINDS R01NS076467; NINDS U01NS090449; NIGMS P41GM10371; Multidisciplinary University Research Initiative Army Research Office |
PMID:30715234 | Free, Available for download, Freely available | SCR_023032 | 2026-02-14 02:05:00 | 0 | ||||||||
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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 | 2026-02-14 02:03:48 | 1582 | |||||||
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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 | 2026-02-14 02:03:48 | 0 | ||||||||
|
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 | 2026-02-14 02:04:13 | 358 | ||||||||
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MUMmer Resource Report Resource Website 100+ mentions |
MUMmer (RRID:SCR_018171) | data processing software, alignment software, software application, software resource, image analysis software | Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes. | Align, genome, DNA, protein, sequence, , bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: MUMmerGPU |
NLM R01 LM06845; NSF IIS 9902923; NIAID N01 AI15447 |
PMID:14759262 | Free, Available for download, Freely available | OMICS_14554, biotools:mummer | https://github.com/mummer4/mummer https://bio.tools/mummer https://sources.debian.org/src/mummer/ |
SCR_018171 | MUMmer4, MUMmer 3.0 | 2026-02-14 02:03:34 | 480 | |||||
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NetMHCpan Server Resource Report Resource Website 100+ mentions |
NetMHCpan Server (RRID:SCR_018182) | data access protocol, software resource, web service | Web server for quantitative prediction of peptide binding to any MHC molecule of known sequence using artificial neural networks. Characterizes binding specificity of given major histocompatibility complex molecule and predicts peptide length profile and peptide binding affinity. NetMHCpan 3.0 is improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets. NetMHCpan 4.0 is trained on naturally eluted ligands and on peptide binding affinity data. NetMHCpan-4.1 server predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks (ANNs). | Quantitative prediction, peptide binding, MHC molecule, artificial neural network, Major Histocompatibilty Complex, peptide length, peptide binding affinity, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Agencia Nacional de Promoción Científica y Tecnológica ; Argentina ; NIAID |
PMID:19002680 PMID:28978689 |
Free, Available for download, Freely Available | biotools:netmhcpan | https://bio.tools/netmhcpan https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/ |
SCR_018182 | NetMHCpan 1.0, NetMHCpan 3.0, NetMHCpan 2.0, NetMHCpan 4.1, NetMHCpan 4.0, NetMHCpan | 2026-02-14 02:03:28 | 138 | |||||
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Recombination Detection Program Resource Report Resource Website 100+ mentions |
Recombination Detection Program (RRID:SCR_018537) | RDP | data analysis software, software resource, data processing software, software application | Software package to analyse nucleotide sequence data and identify evidence of genetic recombination. RDP3 is version of RDP program for characterizing recombination events in DNA-sequence alignments. RDP4 is version of RDP program for detection and analysis of recombination patterns in virus genomes. | DNA sequence, alignment, phylogenetic tree, nucleotide analysis, sequence data analysis, genetic recombination identification, DNA sequence alignment, recombinant pattern analysis, virus genome | Wellcome Trust ; Fund for Scientific Research Flanders ; South African Centre of High Performance Computing ; European Research Council ; Spanish Ministry of Science and Education ; South African National Research Foundation ; University of Cape Town ; Polyomielitis Research Foundation ; Carnergie Corporation ; NIAID AI090970; NIGMS U01 GM110749; NIAID AI100665 |
PMID:27774277 PMID:20798170 |
Free, Available for download, Freely available | SCR_018537 | Recombination Detection Program, RDP4, RDP3 | 2026-02-14 02:03:21 | 483 | |||||||
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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 | 2026-02-14 02:02:47 | 987 | |||
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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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CEDAR Workbench Resource Report Resource Website 1+ mentions |
CEDAR Workbench (RRID:SCR_016270) | data or information resource, software resource, portal, web application | Web application for creating, collecting, testing, and sharing metadata. It provides templates for metadata models or structures, and is capable of testing those models quickly using real data. | metadata, share, collect, capture, model, structure, workspace, workflow, pipeline | has parent organization: Center for Expanded Data Annotation and Retrieval | NIAID U54 AI117925 | Freely available, Account required, Tutorial available | SCR_016270 | CEDAR suite, Center for Expanded Data Annotation and Retrieval Workbench, CEDAR tools | 2026-02-14 02:03:14 | 1 | ||||||||
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Datamonkey Resource Report Resource Website 1000+ mentions |
Datamonkey (RRID:SCR_010278) | data access protocol, software resource, source code, web service | Web-based suite of phylogenetic analysis tools for use in evolutionary biology. Web application for comparative analysis of sequence alignments using statistical models. Used for analyzing evolutionary signatures in sequence data. Datamonkey 2.0 provides curated collection of methods for interrogating coding-sequence alignments for imprints of natural selection, packaged as a responsive (i.e. can be viewed on tablet and mobile devices), fully interactive, and API-enabled web application. | comparative analysis of sequence alignments, analyzing evolutionary signatures, sequence data, | has parent organization: University of California at San Diego; California; USA | NIGMS R01 GM093939; NIGMS U01 GM110749; NSF ; NIAID AI43638; NIAID AI47745; NIAID AI57167; University of California at San Diego ; Canadian Institutes of Health Research |
PMID:15713735 PMID:20671151 PMID:29301006 |
Free, Available for download, Freely available | nlx_156937 | https://github.com/veg/datamonkey-js | SCR_010278 | , Datamonkey 2.0, datamonkey.org | 2026-02-14 02:01:56 | 1120 | |||||
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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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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant 2U24DK097771-09.
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