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Proteinpaint

ProteinPaint it's a public web service at https://proteinpaint.stjude.org/. It was initially designed to visualize cancer coding mutations (Nature Genetics 2016), and later expanded to support more genomic data types from cancer (Cancer Cell 2021). At the core it is a genome browser to run different tracks on, and visualize diverse types of molecular and omics data at a genomic locus. Lately we're also focusing on population science, implementing data dictionaries, sample filtering, and biostatistics analysis, in the Clinical data browser. We also developed the ProteinPaint BAM track for read alignment visualization and variant genotyping.

Customer References

Installation: installation documentation for customers

Build: how to obtain or build Proteinpaint as a Docker image

• Option A: Pull a Prebuilt Image (Recommended)
• Option B: Use NPM
• Option C: Build from Source

ProteinPaint URL parameters

Many ProteinPaint features can be triggered or customized via URL parameters, resulting in a view that can be bookmarked or shared. URL parameters consist of “key=value” pairs. The keys are listed below, and are case-insensitive. File paths begin from but not include the TP directory on the ProteinPaint server.

• Protein view
• Genome Browser
• Non-genome browser features

Plots

• Scatter Plot
• Summary Plot
• Matrix
• Survival Plot
• Violin Plot

Posters

• Survivorship portal poster for KIDS2023