Logistic Regression for Differential Expression

This GitHub repository contains the code for reproducing the analysis and figures in Ntranos, Yi et al., 2019. Parts of the analysis were performed in python and others in R.

Getting Started

For tutorials on using logistic regression for CD45, one can use 10x_example-logR.

For the simulations and analysis in R, simulations/RSEM/R provides the R code for performing logistic regression. The Snakefile contains an overview of the workflow, from creating the simulations to running the analysis and plotting benchmark curves.

Accessing simulation data

Due to the large size of the simulations, we placed the quantifications and counts for the simulations in a separate figshare repository: https://figshare.com/articles/Single_Cell_RNA-Seq_Simulations_for_Ntranos_Yi_et_al_2019/7108364