A program that returns the outlier cellline-drug pairs in PSets in PharmacoGx based on how large the variance between viability measurements are for identical concentrations of dose response curves within the context of each tissue. This program prints the outliers for each tissue, the number of replicate assays total for the tissue (from which the outliers are taken), a histogram plotting the standard deviation of the normalized variances for the tissue, and the dose response curves of the outliers for each tissue. It also creates a data frame at the very end with the outliers for the entire dataset by combining the outliers from each tissue (outliers_all_tissues). This program has been tested on 7 PSets downloaded from ORCESTRA (CCLE_2015, GDSC v2, GRAY2017, FIMM, gCSI_2019, UHN_Breast, CTRPv2) so far and works on 6 of them (CCLE_2015 has a different naming pattern for the replicate experiments compared to the rest of the datasets). Find info on the replicate naming pattern here and all the logged outliers as of August 11, 2025: https://docs.google.com/document/d/1M9Mr5r51QLPTnLrcnqPU1MBXObuftwqRjp0r2_u_yK8/edit?tab=t.0
-
Notifications
You must be signed in to change notification settings - Fork 0
bhklab/pset-viability-curve-outlier-detection-by-tissue
Folders and files
Name | Name | Last commit message | Last commit date | |
---|---|---|---|---|
Repository files navigation
About
No description, website, or topics provided.
Resources
Stars
Watchers
Forks
Releases
No releases published
Packages 0
No packages published