kessenbrocklab / Nguyen_Pervolarakis_Nat_Comm_2018

Supplementary software for "Profiling human breast epithelial cells using single cell RNA sequencing identifies cell diversity"

Nguyen_Pervolarakis_Nat_Comm_2018

Supplementary scripts for "Profiling human breast epithelial cells using single cell RNA sequencing identifies cell diversity"

Table of Contents

• Monocle_Analysis
  • Correlation_Analysis_for_Combined_10x_Ordering.R: Analysis used to choose droplet based ordering genes from Supplementary Data 2
  • state_expression_matrix.R: Custom function built to generate a gene expression matrix by State (used in the combined droplet based Monocle ordering - Figure 6)
    • Combined_4000_State_Branch.txt: example of the "state_branch_data" data frame structure required for input into state_expression_matrix.R
    • state_expression_heatamp.R: Custom function used to generate an annotated heatmap of the expression matrix and data frame output by state_expression_matrix.R (not used in manuscript)