Analysis scripts used in the paper "WRN Helicase is a Synthetic Lethal Target in Microsatellite Unstable Cancers" by Chan and Shibue et al. More info here
An rds file containing a list of datasets used in the main analysis (generate_figs.Rmd) is available as a Figshare repo.
-
process_CCLE_MSI_data.R: This script takes the table of MSI calls from the CCLE Phase 2 manuscript (ref) and generates some normalized MSI indel stats used in make_cell_line_info.R
-
make_cell_line_info.R: This script generates the table of cell line features (omics features and dependency scores) used to generate most analysis. This table is saved to WRN_final_cell_line_table.csv
-
WRN_helpers.R: This script is sourced in generate_figs.Rmd and has some simpler stats and plotting helper functions.
-
generate_figs.Rmd: This script generates all figures analyzing the CCLE/Achilles/GDSC data. It takes as input the cell line table mentioned above (Supplementary Table 1), and also takes as input a set of cell line feature matrices from DepMap 18Q4 data release (available here). In the analysis script these are pulled from our internal data server into a data list object "dat". For convenience, we also provide this list saved as an rds file on the Figshare repo.
-
WRN_diff_express.Rmd: This script runs differenital expression analyses on the RNAseq data and generates figures.
-
in_vivo_KM12_analysis.R: Short script to run linear mixed model analysis on in vivo xenograft data.
-
intensity_calcs.Rmd: Runs linear model contrast tests on IF intensity values across cells.
-
WRN_stats_calcs.Rmd: Script that runs some other small-scale t-test and ANOVA stats.