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Strategy guide for HED Annotation. Framework for systematically describing laboratory and real world events.HED tags are comma separated path strings. Organized in forest of groups with roots Event, Item, Sensory presentation, Attribute, Action, Participant, Experiment context, and Paradigm. Used for preparing brain imaging data for automated analysis and meta analysis. Applied to brain imaging EEG, MEG, fNIRS, multimodal mobile brain or body imaging, ECG, EMG, GSR, or behavioral data. Part of Brain Imaging Data Structure standard for brain imaging.
Proper citation: HED Tags (RRID:SCR_014074) Copy
https://skyline.gs.washington.edu/labkey/project/home/software/Skyline/begin.view
Software tool as Windows client application for targeted proteomics method creation and quantitative data analysis. Open source document editor for creating and analyzing targeted proteomics experiments. Used for large scale quantitative mass spectrometry studies in life sciences.
Proper citation: Skyline (RRID:SCR_014080) Copy
http://www.originlab.com/index.aspx?go=PRODUCTS/Origin
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 4, 2025.Software application for data analysis and graphing. Origin contains a variety of different graph types, including statistical plots, 2D and 3D vector graphs, and counter graphs. More advance version is OriginPro which offers advanced analysis tools and Apps for Peak Fitting, Surface Fitting, Statistics and Signal Processing.
Proper citation: Origin (RRID:SCR_014212) Copy
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.
Proper citation: The Immunology Database and Analysis Portal (ImmPort) (RRID:SCR_012804) Copy
http://statistika.mfub.bg.ac.rs/interactive-linegraph/
Interactive web based tool for creating line graphs for scientific publications. Users can view different summary statistics, examine lines for any individual in data, focus on time points or groups of interest, and view changes between any two time points and conditions.
Proper citation: Interactive Line Graph (RRID:SCR_018334) Copy
https://huygens.science.uva.nl/PlotsOfData/
Web app for visualizing data together with their summaries. Visualizes data and statistics to enable comparison of experimental conditions. Written in R and uses packages including shiny, ggplot2, dplyr, tidyr, readr, magrittr, ggbeeswarm, readxl, DT. Github page of PlotsOfData can be used to trace changes between different versions.
Proper citation: PlotsOfData (RRID:SCR_018333) Copy
https://webs.iiitd.edu.in/raghava/coronavir
Web based platform on COVID-19 to maintain predicted diagnostic, drug and vaccine candidates and computational resources on novel coronavirus SARS-CoV-2 and its resulting disease COVID-19. Provides collected and organized information from literature and other resources from internet, links to appropriate literature . Integrated multi-omics repository dedicated to current genomic, proteomic, diagnostic and therapeutic knowledge about coronaviruses.
Proper citation: CoronaVIR (RRID:SCR_018338) Copy
https://professional.diabetes.org/content-page/covid-19
Web page created by American Diabetes Association. Contains resources and information about COVID-19 for diabetes professionals and patients. ADA also provides online forum, webinar series and podcast. Online forum to exchange questions, answers, and best practices with leading clinicians from diabetes community. All ADA members can contribute, and any interested health professional can read forum and responses.
Proper citation: American Diabetes Association COVID-19 Resources and Webinar Series (RRID:SCR_018346) Copy
Open source project to harness scientific and public health potential of pathogen genome data. Provides continually updated view of publicly available data alongside powerful analytic and visualization tools for use by community. Used to aid epidemiological understanding and improve outbreak response. Open source SARS-CoV-2 genome data and analytic and visualization tools.
Proper citation: Nextstrain (RRID:SCR_018223) Copy
https://www.ebi.ac.uk/ena/pathogens/covid-19
Data collection related to COVID-19 held at EMBL-EBI , including sequences of outbreak isolates and records related to coronavirus biology, protein expression, protein sequence, protein structure, proteome and translatome data and literature.
Proper citation: EMBL-EBI Pathogens - COVID-19 (RRID:SCR_018343) Copy
https://bigd.big.ac.cn/ncov/?lang=en
Bioinformation related to COVID-19. Site developed and maintained by China National Center for Bioinformation. Collection of sequences, genome variations, publication, clinical resource data.
Proper citation: 2019 Novel Coronavirus Resource (2019nCoVR) by China National Center for Bioinformation (RRID:SCR_018342) Copy
Portal to make cancer related proteomic datasets easily accessible to public. Facilitates multiomic integration in support of precision medicine through interoperability with other resources. Developed to advance our understanding of how proteins help to shape risk, diagnosis, development, progression, and treatment of cancer. One of several repositories within NCI Cancer Research Data Commons which enables researchers to link proteomic data with other data sets (e.g., genomic and imaging data) and to submit, collect, analyze, store, and share data throughout cancer data ecosystem. PDC provides access to highly curated and standardized biospecimen, clinical, and proteomic data, intuitive interface to filter, query, search, visualize and download data and metadata. Provides common data harmonization pipeline to uniformly analyze all PDC data and provides advanced visualization of quantitative information. Cloud based (Amazon Web Services) infrastructure facilitates interoperability with AWS based data analysis tools and platforms natively. Application programming interface (API) provides cloud-agnostic data access and allows third parties to extend functionality beyond PDC. Structured workspace that serves as private user data store and also data submission portal. Distributes controlled access data, such as patient-specific protein fasta sequence databases, with dbGaP authorization and eRA Commons authentication.
Proper citation: Proteomic Data Commons (RRID:SCR_018273) Copy
https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/
Collection of SARS-CoV-2 sequences currently available in GenBank genetic sequence database and Sequence Read Archive. Updated as additional sequences are released.
Proper citation: SARS-CoV-2-Sequences (RRID:SCR_018319) Copy
Portal to share hCoV-19 genome sequences. Collection of genome sequences and related clinical and epidemiological data associated with coronavirus hCoV-19. Global repository of SARS-CoV-2 genomes. Initiative involves public-private-partnerships between Freunde of GISAID and governments of Federal Republic of Germany, Singapore and United States of America, with support from private and corporate philanthropy.International database of hCoV-19 genome sequences and related clinical and epidemiological data. Resource for influenza and hCoV-19 data.
Proper citation: Global Initiative on Sharing All Influenza Data (RRID:SCR_018251) Copy
https://amp.pharm.mssm.edu/covid19/
Software tool as interface to submit, serve, and analyze COVID19 related gene and drug sets. Collection of gene and drug sets related to COVID-19 research contributed by community.
Proper citation: COVID-19 Crowd Generated Gene and Drug Set Library (RRID:SCR_018252) Copy
https://github.com/sysu-yanglab/TDimpute
Software tool to transfer learning based deep neural network to impute missing gene expression data from DNA methylation data.
Proper citation: TDimpute (RRID:SCR_018306) Copy
Web provides tools for modeling 3D structures of molecules and complexes containing carbohydrates including oligosaccharide conformation modeling and glycoprotein 3D structure modeling. Used to simplify prediction of three dimensional structures of carbohydrates and macromolecular structures involving carbohydrates.
Proper citation: GLYCAM-Web (RRID:SCR_018260) Copy
https://CRAN.R-project.org/package=biomod2
Software R package for species distribution modeling, calibration and evaluation, ensemble of models, ensemble forecasting and visualization.
Proper citation: biomod2 (RRID:SCR_018246) Copy
Web tool to perform gene set enrichment testing. Used to test for predefined biologically relevant gene sets that contain more significant genes from experimental dataset than expected by chance. Logistic regression approach for identifying enriched biological groups in gene expression data.
Proper citation: LRPath (RRID:SCR_018572) Copy
http://theparkerlab.org/tools/isleteqtl/
Web tool for exploring variants in islet expression quantitative trait loci. Data is result of collaboration between Michigan University Parker lab, Department of Biostatistics and Center for Statistical Genetics at University of Michigan, National Human Genome Research Institute, Jackson Laboratory for Genomic Medicine, Department of Genetics at University of North Carolina, European Bioinformatics Institute, Department of Preventive Medicine at University of Southern California, and Department of Physiology and Biophysics at University of Southern California.
Proper citation: Islet eQTL Explorer (RRID:SCR_018692) Copy
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