D3Oncoprint
D3Oncoprint: a standalone software to visualize and dynamically explore annotated genomic mutation files
Overview: A Standalone Software to Visualize and Dynamically Explore Annotated Genomic Mutation Files
D3Oncoprint supports interactive exploration of genomic datasets. This standalone software works on local machines -- no programming skills are required. Researchers can use it to analyze annotated genomic mutation files.
D3Oncoprint includes curated lists of variants lists from CIViC, My Cancer Genome, and FDA-approved drug indication listings. These genomic datasets facilitate biomedical discovery and application. D3Oncoprint also includes curated gene lists that can be used to explore commonly investigated biological processes (i.e., BioCarta pathways, FoundationOne cancer panels).
Our software provides a flexible way to explore variant mutation profile inputs. Interactive visualization with biological and medical annotation is central to its processes. This allows biomedical investigators to easily access complex genomic data. We hope that this will empower researchers to translate information from the collected data sets and apply it to new biological insights and clinical applications.
IMPORTANT NOTE: Some operating systems (OS) may not allow default installation of "unofficial apps" downloaded from the internet. This issue is not specific to the D3Oncoprint executable file; it depends on your OS’s security requirements. If the D3Oncoprint executable file doesn't seem to run, please inspect your OS’s security warnings. You may need to change the system settings to allow the D3Oncoprint application to be downloaded and executed. This issue should only occur once; OS security settings will then be saved on your machine.
Disclaimer: This resource is intended for purely research purposes. It should not be used for emergencies or medical or professional advice.
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Read more about the application
D3Oncoprint: Stand-Alone Software to Visualize and Dynamically Explore Annotated Genomic Mutation Files
Alida Palmisano, Yingdong Zhao and Richard Simon, JCO Clinical Cancer Informatics, 2018. nr. 2, p. 1-9
Software Screenshots
(a) Data Input tab, used by the user to give the project a name and select the input files from the files system.
(b) Selection of the data columns to match the content of the input files to the fields required by D3Oncoprint to generate the interactive plots.
(c) An example of a generated HTML page: an interactive heatmap, exploration buttons and a dynamic datatable displaying all variants across the input samples. More details about D3Oncoprint interface are available in the User Manual.
D3Oncoprint heatmaps for the TCGA-CHOL cohort. Rows represent genes, and columns represent samples. The default view (a) sorts the genes by total mutation count across all the samples, and it sorts the samples by total mutation count across all the genes. Different types of mutations are identified by different colors in the grey heatmap (point mutations, insertion, deletions, etc). Moving the cursor on a cell with mutation will display a popup with some information about that mutation. Rows can be dragged up/down by clicking and moving the gene name label. Columns can be dragged left/right by clicking and moving the sample name label. Phenotypes are listed in the lower part of the heatmap, and phenotypes' labels act like sorting buttons: clicking any of these buttons will move around the columns separating the samples according to the clicked phenotype value (Vital status (b) and Gender (c)). More details about the interpretation of the different maps are included in the User Manual.