This repository contains the code for the analysis of the deep mutational screening data from the ResMAP project as detailed in the publication:
- Richard J. Wall, Stuart A. MacGowan, Irene Hallyburton, Sowmya Ajay Castro, Gourav Dey, Rachel Milne, Stephen Patterson, Jody Phelan, Aisha Syed, Natalie Wiedemar and Susan Wyllie. ResMAP – a saturation mutagenesis platform enabling parallel profiling of target-specific resistance conferring mutations in Plasmodium. Submitted.
ResMAP aims to identify mutations in Plasmodium that confer resistance to antimalarial drugs, providing insights critical for developing novel therapeutics.
The quantification, analysis, and data directories in this repository encompass the entire workflow from data quantification to analysis:
quantification: Containscount-sequences.pyfor library quantification.analysis: R Markdown notebooks for data analysis.data: Includes raw and processed data files.
The data directory structure is as follows:
PfKRS-mutlib-final-calculations-*.tsv: Library counts for various conditions.PkmutWTd1_1pc.sam: Sample sequencing data.pfkrs-n20-library.csv: Library design file.
count-sequences.py in the quantification directory is used for counting mutants. See the quantification README for usage details.
R Markdown notebooks in the analysis directory outline the analysis workflow. Numbered sequentially, these notebooks are detailed in the analysis README, with rendered versions available for viewing.
This repository is licensed under the MIT License. See the LICENSE file for details.