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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Tracer Resource Report Resource Website 1000+ mentions |
Tracer (RRID:SCR_019121) | data analysis software, data processing software, data visualization 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 | European Union Seventh Framework Programme ; NIAID R01 AI107034; NIAID U19 AI135995; NSF DMS 1264153; Wellcome Trust |
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 | 2026-09-12 12:59:10 | 1598 | |||||||
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DatA Tag Suite Resource Report Resource Website |
DatA Tag Suite (RRID:SCR_019236) | DATS | data or information resource, narrative resource, software resource, software toolkit, 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 | ELIXIR EXCELERATE ; ELIXIR-UK ; NIAID U24 AI117966 |
PMID:28585923 | Free, Freely available | SCR_019236 | 2026-09-12 12:59:11 | 0 | ||||||||
|
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 | 2026-09-12 12:58:28 | 159 | |||||
|
SPICE Resource Report Resource Website 50+ mentions |
SPICE (RRID:SCR_016603) | SPICE | data analysis software, data processing software, data visualization software, software application, software resource | Software application for data mining and visualization. Used for analyzes of large FLOWJO data sets from polychromatic flow cytometry and organizing the normalized data graphically. | data, mining, visualization, analysis, polychromatic, flow, cytometry, dataset, normalized, graphically, bio.tools |
is listed by: NIAID is listed by: Debian is listed by: bio.tools |
NIAID ; NIH |
PMID:21265010 | Free, Available for download, Freely available | biotools:spice | https://bio.tools/spice | SCR_016603 | Simplified Presentation of Incredibly Complex Evaluations | 2026-09-12 12:58:42 | 72 | ||||
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Discovar assembler Resource Report Resource Website 10+ mentions |
Discovar assembler (RRID:SCR_016755) | Discovar | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for variant calling with reference and de novo assembly of genomes. The heart of DISCOVAR is a de novo genome assembler which can generate de novo assemblies for both large and small genomes. | variant, calling, reference, de novo, assembly, genome, genetic, human, sequence, analysis |
is listed by: OMICtools has parent organization: Broad Institute |
NHGRI R01 HG003474; NHGRI U54 HG003067; NIAID HHSN272200900018C |
PMID:25326702 | Free, Available for download, Freely available | SCR_016755 | Discovar de novo, Discovar | 2026-09-12 12:58:44 | 20 | ||||||
|
proMODMatcher Resource Report Resource Website 1+ mentions |
proMODMatcher (RRID:SCR_017219) | data analysis software, data processing software, software application, software resource | 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; NIAID U19 AI118610; NIA R01 AG046170 |
biotools:modmatcher | https://bio.tools/modmatcher | SCR_017219 | probabilisticMulti Omics DataMatcher | 2026-09-12 12:58:50 | 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 | simulation software, software application, software resource | 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 | NIAID AI116794; NIDDK DK112217; NLM LM012601 |
PMID:29218887 | Free, Available for download, Freely available | SCR_017140 | Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions | 2026-09-12 12:58:49 | 0 | |||||||
|
ArchR Resource Report Resource Website 100+ mentions |
ArchR (RRID:SCR_020982) | data analysis software, data processing software, software application, software resource, software toolkit | 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 | American Society of Hematology Scholar Award ; Defense Advanced Research Project Agency ; International Collaborative Award ; NCI R35 CA209919; NCI U2C CA233311; NHGRI RM1 HG007735; NHGRI UM1 HG009436; NHGRI UM1 HG009442; NIAID U19 AI057266; NIA K99 AG059918; 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 | 2026-09-12 12:59:49 | 424 | ||||||||
|
MUMmer Resource Report Resource Website 500+ mentions |
MUMmer (RRID:SCR_018171) | alignment software, data processing software, image analysis software, software application, software resource | 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 |
NIAID N01 AI15447; NLM R01 LM06845; NSF IIS 9902923 |
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 | 2026-09-12 12:58:58 | 547 | |||||
|
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 | 2026-09-12 12:58:58 | 169 | |||||
|
Recombination Detection Program Resource Report Resource Website 500+ mentions |
Recombination Detection Program (RRID:SCR_018537) | RDP | data analysis software, data processing software, software application, software resource | 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 | Carnergie Corporation ; European Research Council ; Fund for Scientific Research Flanders ; NIAID AI090970; NIAID AI100665; NIGMS U01 GM110749; Polyomielitis Research Foundation ; South African Centre of High Performance Computing ; South African National Research Foundation ; Spanish Ministry of Science and Education ; University of Cape Town ; Wellcome Trust |
PMID:27774277 PMID:20798170 |
Free, Available for download, Freely available | SCR_018537 | Recombination Detection Program, RDP4, RDP3 | 2026-09-12 12:59:02 | 507 | |||||||
|
CEDAR Workbench Resource Report Resource Website 1+ mentions |
CEDAR Workbench (RRID:SCR_016270) | data or information resource, portal, software resource, 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 | 2026-09-12 12:58:37 | 2 | ||||||||
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HIV Molecular Immunology Database Resource Report Resource Website 1+ mentions |
HIV Molecular Immunology Database (RRID:SCR_002893) | HIV Molecular Immunology Database | data or information resource, database | An annotated, searchable collection of HIV-1 cytotoxic and helper T-cell epitopes and antibody binding sites, plus related tools and information. The goal of this database is to provide a comprehensive listing of defined HIV epitopes. These data are also printed in the HIV Molecular Immunology compendium, which is updated yearly and provided free of charge to scientific researchers, both by online download and as a printed copy. The data included in this database are extracted from the HIV immunology literature. HIV-specific B-cell and T-cell responses are summarized and annotated. Immunological responses are divided into three sections, CTL (CD8+), T helper (CD4+), and antibody. Within these sections, defined epitopes are organized by protein and binding sites within each protein, moving from left to right through the coding regions spanning the HIV genome. We include human responses to natural HIV infections, as well as vaccine studies in a range of animal models and human trials. Responses that are not specifically defined, such as responses to whole proteins or monoclonal antibody responses to discontinuous epitopes, are summarized at the end of each protein sub-section. Studies describing general HIV responses to the virus, but not to any specific protein, are included at the end of each section. The annotation includes information such as cross-reactivity, escape mutations, antibody sequence, TCR usage, functional domains that overlap with an epitope, immune response associations with rates of progression and therapy, and how specific epitopes were experimentally defined. Basic information such as HLA specificities for T-cell epitopes, isotypes of monoclonal antibodies, and epitope sequences are included whenever possible. All studies that we can find that incorporate the use of a specific monoclonal antibody are included in the entry for that antibody. A single T-cell epitope can have multiple entries, generally one entry per study. Finally, tables and maps of all defined linear epitopes relative to the HXB2 reference proteins are provided. Alignments of CTL, helper T-cell, and antibody epitopes are available through the search interfaces. Only responses to HIV-1 and HIV-2 are included in the database. | cytotoxic t cell, cytotoxic t lymphocyte, helper t-cell, antibody, binding site, epitope, t cell epitope, human immunodeficiency virus, immunology, molecule, genome, protein, alignment, b-cell, t-cell, annotation, ctl, t helper, coding region, cross-reactivity, escape mutation, antibody sequence, tcr usage, functional domain, immune response, progression, therapy | has parent organization: HIV Databases | Human immunodeficiency virus | NIAID | nif-0000-02965 | http://hiv-web.lanl.gov/immunology/ | SCR_002893 | Human Immunodeficiency Virus Molecular Immunology Database | 2026-09-12 01:01:27 | 2 | |||||
|
Nonhuman Primate HIV/SIV Vaccine Trials Database Resource Report Resource Website |
Nonhuman Primate HIV/SIV Vaccine Trials Database (RRID:SCR_002274) | data or information resource, database | An overview of HIV and SIV vaccine trials and their outcomes. It was developed as a tool for compilation, search and comparison of published studies on SIV, HIV and SHIV vaccine trials in nonhuman primates. We used a set of criteria to scan Pubmed for relevant studies to enter into the database. In selecting studies for entry, priority was given to recently published studies in journals generally regarded as the primary source of information pertaining to HIV and SIV vaccine research in nonhuman primates. In most cases, we give priority to challenge studies, where the animals received a live virus to measure the "efficacy" of the immunogen(s) inoculated during the course of the investigation. The HIV Sequence Database focuses on five primary goals: *Collecting HIV and SIV sequence data (all sequences since 1987) *Curating and annotating this data, and making it available to the scientific community *Computer analysis of HIV and related sequences *Production of software for the analysis of (sequence) data *Publication of the data and analyses on this site and in a yearly printed publication, the HIV sequence Compendium, which is available free of charge | drug, trial, vaccine, human immunodeficiency virus, simian immunodeficiency virus | has parent organization: HIV Databases | Human immunodeficiency virus, Simian immunodeficiency virus | NIAID | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20999 | http://hiv-web.lanl.gov/cgi-bin/vaccine/public/index.cgi | SCR_002274 | HIV/SIV Trials Vaccine DB, HIV/SIV Trials Vaccine Database | 2026-09-12 01:01:25 | 0 | |||||
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MG-RAST Resource Report Resource Website 1000+ mentions |
MG-RAST (RRID:SCR_004814) | MG RAST | analysis service resource, data analysis service, production service resource, service resource | An automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data. The server primarily provides upload, quality control, automated annotation and analysis for prokaryotic metagenomic shotgun samples. | metagenome, base pair, sequence, phylogenetic, functional analysis, data sharing, metadata, protein, micro biome, analysis platform, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools has parent organization: Argonne National Laboratory |
NIAID contract HHSN272200900040C; DOE contract DE-AC02-06CH11357 |
PMID:18803844 | Acknowledgement requested, Public, Account required | OMICS_01456, biotools:mg-rast | http://metagenomics.nmpdr.org, https://bio.tools/mg-rast | SCR_004814 | The Metagenomics RAST server, Metagenomics RAST, MG-RAST - metagenomics analysis server | 2026-09-12 01:01:34 | 1165 | ||||
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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 | 2026-09-12 01:03:01 | 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 | NHLBI HL131560; NHLBI HL139897; NIAID ; UCSF Marcus Award ; UCSF Nina Ireland Program award |
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 | 2026-09-12 01:03:03 | 411 | |||||||
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DADA2 Resource Report Resource Website 1000+ 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 |
NIAID R01AI112401; NSF ; Samarth Foundation |
PMID:27214047 | Free, Available for download, Freely available | https://bioconductor.org/packages/dada2/ | SCR_023519 | 2026-09-12 01:03:05 | 1134 | |||||||
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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, | National Institutes of Health ; Department of Health and Human Services ; NIAID ; Washington University School of Medicine |
PMID:23748956 | Free, Available for download, Freely available | SCR_023689 | 2026-09-12 01:03:05 | 3 | |||||||||
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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 | 2026-09-12 01:02:50 | 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 U24DK097771.
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