Last updated: 2023-04-10
Checks: 1 1
Knit directory: duplex_sequencing_screen/
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HTML.
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Note that you need to be careful to ensure that all relevant files for
the analysis have been committed to Git prior to generating the results
(you can use wflow_publish
or
wflow_git_commit
). workflowr only checks the R Markdown
file, but you know if there are other scripts or data files that it
depends on. Below is the status of the Git repository when the results
were generated:
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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 view
preliminary BCRABL Imatinib and Asciminib heatmaps
Click here and to view iL3 independence data and here to view iL3 independence heatmap
Click here to view error rates without barcodes, with single strand consensi, and with duplex consensus sequencing.
Click here to view the results of the BCRABL Library transduced in K562 Cells
Click here to
view analyses of the CDFs of our saturating mutagenesis libraries. These
show how even or uneven the libraries are at different stages of the
screening process.
Click here to view
analyses in which we compared base editing and saturating mutagenesis
data on ABL. This is followed by analysis in which we decide on filter
cutoffs for enrichment scores to detect signficantly depleting mutants
that drop out for IL3 independence in BaF3s.
Click here to view
analyses in which we predicted admixtures of mutants made by sgRNAs in
Base Editing Screens. We then used the saturating mutagenesis data to
predict the fitness of these sgRNAs.
What is in each directory: