The release of the Treehouse CARE pipeline marks a significant milestone in Treehouse work. Along with the prior public release of our data compendium, the release of the CARE pipeline makes it possible for bioinformatics and genomics researchers at any institution to perform on-demand automated Treehouse analysis on their own data. 

This is an important step towards Treehouse analysis becoming more widely used in the pediatric cancer community. 

The CARE pipeline is Dockerized, meaning that it does not require specialized software expertise to install or use. It produces JavaScript Object Notation (JSON) documents containing all calculations, and a human-friendly HTML report of the automated results with space for analysts to add their findings; in addition, all the code is presented in Jupyter notebooks (Python or R) allowing interactive exploration.

Before the CARE pipeline was publicly available, the only way a researcher could get Treehouse analysis results was to send Treehouse their data for analysis. The data transfer process could be time-consuming and the analysis required the personal attention of Treehouse researchers. This resulted in Treehouse automated analysis being offered for only a limited number of cases. 

Now, with the public release of CARE, this analysis can instead take place at researchers’ institutions without the need to coordinate with Treehouse. 

We are excited to see our analysis used by others and to broaden the potential for our data to help more children with cancer!