Training material for Galaxy tutorial "Calculating CHEK2 variant effect scores from MAVE data with CountESS"

This dataset supports the Galaxy Training Network tutorial “Calculating CHEK2 variant effect scores from MAVE data with CountESS”.

It contains input files for running a saved CountESS workflow in Galaxy to calculate RAD53 Complementation Scores (RCS) for coding SNVs in the human CHEK2 gene. The workflow uses variant frequency summaries derived from a multiplexed assay of variant effect (MAVE) study deposited in MaveDB as urn:mavedb:00001203-a-2.

Files included:

• chek2_frequency_summary.csv: preprocessed CHEK2 variant frequency summary table containing variant identifiers and average frequencies before and after yeast complementation selection.
• chek2_rcs_countess.ini: CountESS workflow configuration generated from the CountESS GUI. The workflow loads the frequency table, calculates RCS_this_SNV = log2(Ave_S1toS4_x1000 / Ave_LibAandB_x1000), and writes the resulting scores to CSV.

The calculated RCS values reproduce the RCS_this_SNV column from the corresponding MaveDB score set. These files are intended for training and demonstration of reproducible CountESS workflow execution in Galaxy.