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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
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
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
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://www.nitrc.org/projects/reproman/
Software tool to simplify creation and management of computing environments in Neuroimaging.
Proper citation: ReproMan (RRID:SCR_018468) Copy
http://www.evolvedmicrobe.com/CurveFitter/
Software tool for growth curve fitting and visualization. Program allows to fit growth curve using simple GUI or advanced scripting environment. Used to fit growth curves generated for data collected in microtiter plates or elsewhere.
Proper citation: CurveFitter (RRID:SCR_018461) Copy
https://github.com/embl-cba/fiji-plugin-bigDataProcessor/blob/master/README.md
Software tool for visual inspection and processing of big image data. Enables loading of Tiff and Hdf5 based image data. BDC supports cropping and saving of big image data including binning and bit depth conversion. Used for analysis of TB sized image data like light sheet microscopy or electron microscopy.
Proper citation: Big Data Processor (RRID:SCR_018484) 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
https://med.stanford.edu/starr-tools.html
Platform developed and operated by Stanford Medicine Research IT team for working with clinical data for research purposes. Permits collection and aggregation of all clinical data generated at Stanford for care purposes, and articulates formal approval process each research project must follow in order to obtain and work with this data for research purpose. Home of stride/web tools for Cohort Discovery and Chart Review.
Proper citation: Stanford Medicine Research Data Repository (RRID:SCR_018686) Copy
https://www.ucl.ac.uk/ncl-disease/mutation-and-patient-database
Collection of published mutations and sequence variations in genes that cause Neuronal Ceroid Lipofuscinoses together with unpublished data included with permission. There are two tables for each human NCL disease gene - Patient Datasheets list all published or reported patients and families, and Mutation Datasheets list all published or reported mutations, cross-referenced to patient table. Datasheets are available to view or download as excel files for off-site use to aid local needs or interests. Database follows mutation nomenclature recommendations of Human Genome Variation Society.
Proper citation: Mutation and Patient Database (RRID:SCR_018806) Copy
https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/
Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data.
Proper citation: RiboTaper (RRID:SCR_018880) Copy
Software R package for flexibly restructuring and aggregating data.
Proper citation: reshape (RRID:SCR_018983) Copy
Web tool for visualization of genome annotations across large phylogenetic trees.Used for visualization and exploration of functionally annotated microbial tree of life. Integrates taxonomic, phylogenetic and functional annotation data from bacterial and archaeal genomes.
Proper citation: Annotree (RRID:SCR_018980) Copy
http://easybioai.com/sc2disease/
Manually curated database of single cell transcriptome for human diseases. scRNA-seq database derived from numerous human studies. Provides researchers with encyclopedia of biomarkers at level of genes, cells, and diseases.
Proper citation: SC2diseases (RRID:SCR_019093) Copy
https://github.com/auranic/ClinTrajan
Software Python package for analysis of trajectories in clinical datasets.
Proper citation: ClinTrajAn (RRID:SCR_019018) Copy
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