Single Cell analysis of Antigen Expression in the African Trypanosome

Code Supporting An allele-selective inter-chromosomal protein bridge supports monogenic antigen expression in the African trypanosome

Affiliation

Wellcome Centre for Anti-Infectives Research
School of Life Sciences, University of Dundee

Instructions

The analysis has been performed in a Python Jupyter Notebook with the rpy2 package to call R functions. 
The environment for the Jupyter Notebook is saved in env.txt.
The R packages used are listed in sessionInfo.txt.

For each experiment, we have two replicates:
VEX1_RNAi_1 & VEX1_RNAi_2 (RNA interference for VEX1)
VEX2_RNAi_1 & VEX2_RNAi_2 (RNA interference for VEX2)
VSG-2_1 & VSG-2_1 (VSG2 expression analysis)
VSG-2_VSG-6_1 & VSG-2_VSG-6_1  (VSG2 and VSG6 expression analysis, control for doublets)

Each experiment tag corresponds to a folder ( with the Cell Ranger Software outputs, not provided
just a placeholder) and Jupyter Notebook (with the analysis code). The notebooks with the "merge" tag
analyse the replicated experiments together.