Open Single-Cell Pediatric Cancer Atlas (OpenScPCA)

Open and collaborative project analyzing data from over 50 pediatric cancer types

About OpenScPCA

OpenScPCA is an open, collaborative project to analyze data from the ScPCA Portal, which currently holds 500 samples from over 50 pediatric cancer types.

This project aims to:

  • Characterize the ScPCA data with analyses such as labeling cell types or identifying recurrent cell states in multiple tumor types.
  • Work on open and collaborative analyses.
  • Build consensus around usage, strengths, and pitfalls of methods and their application to pediatric cancer data.
  • Improve the utility of the ScPCA data for the research community by exploring the creation of new data assets.
Learn more about OpenSCPCA

How it works

Co-develop analysis ideas and approaches

Data Lab members and other contributors work together to shape analysis ideas and select the best approaches to implement analyses.

Write reproducible code to perform analyses

Contributors work on an analysis module within a reproducible research framework set up by the Data Lab.

Participate in the analytical code review process

Contributors participate in the code review process, which helps them improve their programming skills and gain experience collaborating on a code base.

Add analyses to the project

Contributors add their analysis to benefit the broader pediatric cancer community!

Contribute to OpenScPCA

Are you a disease expert, a seasoned computational biologist, or looking to hone your data analysis skills? We welcome your contributions to OpenScPCA!

Fill out the interest form below and receive more information about joining the project.

Benefits of Participating

Access to data and tools

Discover new datasets to advance your research and learn how to use powerful tooling for reproducible research and software development.

Join a supportive community

Connect with the Data Lab and receive ongoing support from our team throughout the project. Meet potential collaborators with diverse skill sets and a variety of expertise!

Develop skills and gain experience

Build your analysis portfolio, develop transferable skills in big data analysis, and gain experience working collaboratively in a large code base.

Contribute to impactful research

Contribute to open science and help build a resource that will benefit a broad community of pediatric cancer researchers. Plus, you may be part of a future publication!

Other ways to get started

Learn more about OpenScPCA

Read our documentation about getting set up, contributing to analyses, using our software platforms and more.

Read more

Join the conversation on GitHub Discussions

Ask questions, discuss big picture ideas, brainstorm, and develop plans for analyses.

Learn more

Explore an example analysis module

Create a local setup and explore how analysis modules are structured, and play with some simulated data or data from the ScPCA Portal.

Explore an example module


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