Modeling glioblastoma heterogeneity as a dynamic network of cell states
Matlab (R2019a)
CVX: Matlab Software for Disciplined Convex Programming
STAG requires an input matrix where each row represents a single cell, and the columns are genes (opt.), barcode, timepoint, treatment and state (opt.) according to:
Genes: Normalized expression values, if states should be assigned within the pipeline.
Barcode: The barcode retrieved for each individual cell.
Timepoint: The timepoint the cell was sampled.
Treatment: Single digit (1,2,...,n). If no treatment, 1 for all cells.
State: Single digit (1,2,...,n) if this has been assigned before. Can also be assigned within the pipeline.
The file "expressionMatrices_20210622.mat" includes barcoded data for the three GBM cell lines U3017MG, U3065MG and U3071MG.
Follow the script main.m
A-matrix with transition and growth rates