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Last updated: 2020-06-07
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Knit directory: duplex_sequencing_screen/
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Duplex Sequencing Spike-Ins
###Click here for the script that reads BCRABL dose response data, and fits it to a 4-parameter dose response curve.
###Click here for the script that reads mutation annotation data and generates dataframes with annotated variants and the correct cell counts
###Click here for initial growth rate plots
###Click here for growth rate plots for ENU mutants
###Click here for analysis looking at whether we achieved our desired depth of coverages
###Click here for analysis looking at how well our data predicts BCRABL clinical abundance compared to conventional IC50s
###Click here for method to obtain confidence intervals on growth rates from IC50 measurements. Plotted alongside observed growth rate data, these confidence intervals show how well our pooled data matches predictions based off of IC50s. (Needs updates in methodology)
###Click here for analyses of replicate to replicate agreement between the spike in replicates. Also includes this analysis for the mutagenesis replicates. Also includes the agreement in observed vs predicted depth of coverages for all sequencing pools. Note: this analysis does not include dosage corrections that improves replicate to replicate heterogeneity.
###Click here to see analysis of predictions based on Enrich2 vs Shendure vs our method
###Click here for our dosing normalization strategy
###Click here for simulations showing enrichment and depletion events in a 3 mutant pool.
###Click here showing the conformity between the growth rates in the presence of drug measured at a low MAF via FACs, sequencing, and via IC50 studies for a single mutant.
Click here to be redirected to the github page that contains all the data and analysis rmd files.
What is in each directory:
- Data: contains data downloaded prior to analyses.
- Output: contains data that the code makes
- Analysis: contains your Rmarkdown files with the code.
- Docs: contain the html output from the Rmd files in the analysis directory.
- Code: contains .R files that are functions that the Rmd files in the analysis folder use.