CTC-smartseq3

Scripts required to replicate analysis of data for the following publication:

File descriptions

environment.yml

• yaml file used to create conda environment in which the analysis was run

environment_exported.yml

• yaml file containing all versions of all packages in conda environment used for these analyses
• exported from environment creating using the environment.yml file (above)

installRdependencies.txt

• R packages installed on the R terminal

zUMIs_CTCsmartseq3.yaml

• yaml file used to run zUMIs
• used the form: zUMIs -y zUMIs_CTCsmartseq3.yaml -d /path/to/zUMIs/scripts -c

processCTC.R

• script used for analysis of scRNA-seq data

ensembleIDtoGeneNameMap.txt

• file mapping mitochondrial gene ID to gene name
• input for processCTC.R