Minor editorial changes

Minor changes requested by the editor. Now, every figure with a box plot has a description of the demarcations of the box and whiskers. Also, most of the raw data has been made available in FigShare (linked in the manuscript and README).

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Other changes/adjustments

• Refined the scripts for setting of the R and Python environments.
• Minor typos in comments.
• Updated Reproduction Guide with link to data sources.

Accepted by Nature Communications

The paper has been accepted to Nature Communications and the changes made for this release are primarily to adjust the text and figures according to the style guides of the journal.

Second full internal review of resubmission

Merge pull request #5 from jhrcook/dusp-analysis

DUSP differential gene expression analysis (Yi-Jang)

Full internal review of comutation project

The main focus of this release was on the last section of the Results where we built models to explain the KRAS allele-specific genetic dependency interaction using comutation events with the allele. There were also minor changes to the rest of the text.

Full internal review of comutation project

This version includes the final analysis where the allele-specific dependency interactions were modeled with covariates for allele-specific comutation events. There are two additional main figures and one supplementary figure.

Full internal review of comutation project

This tag marks the state of the project at the point where comments and edits have been returned by everyone involved including Professor Haigis, Professor Park, Giorgio Melloni, and Doga Gulhan. An exception is the last section for the integration of comutation and DepMap results; this work is still in progress.

Full internal review of comutation project

This tag marks the state of the project at the point where comments and edits have been returned by everyone involved including Professor Haigis, Professor Park, and Giorgio Melloni.

First full draft

The first complete draft of the paper has been sent to Kevin Haigis for review. Minor changes may be made in the mean time, but primarily internal changes.