BradBalderson/Melanoma_manuscript

Contains code for figure panels and analysis for "Systematic analysis of the Transcriptional Landscape of Melanoma Reveals Drug-target Expression Plasticity"

Melanoma transcriptional phenotype switching meta-analysis manuscript

Code for meta-analysis comparing melanoma cell states identified from bulk and scRNA-seq studies in terms of cell states, gene co-expression, and predicted drug sensitivities.

Overview

An overview for each of the directory structure. Analysis summarised in below figure.

For information about individual scripts and notebooks, see docs/index.md.

scripts/

X1_tirosh_trajectory/
    -> Code for the tirosh scRNA-seq patient tumour trajectory analysis.
    
X2_tsoi_vs_tirosh/
    -> Code comparing bulk RNA-seq low-passage cell line states to the 
        tirosh trajectory.
        
X3_tcga_vs_tirosh/
    -> Compares TCGA bulk RNA-seq patient samples to tirosh scRNA-seq 
        patient tumour trajectory.
    
X4_rambow_vs_tirosh/
    -> Compares the rambow PDX scRNA-seq trajectory to the tirosh patient
        scRNA-seq trajectory.
        
X5_drug_analysis/
    -> Performs drug susceptibility analysis for each dataset and compares
        predictions.