Download all the datasets used in the following Supplemental code is given at: https://drive.google.com/file/d/1gK7fZGfEYA9LoTSKp2YrM7hKH2v8qoFi/view?usp=share_link

Supplemental_code/unCTC_datasets  ---> Contain all the datasets used for Study 1, Study 2.
Supplemental_code/fastMNN ---> Seurat fastMNN wrapper pipeline for Study 1 (Count), Study 2 (TPM), Study 2 (Count).
Supplemental_code/Harmony ---> Seurat Harmony wrapper pipeline for Study 1 (Count), Study 2 (TPM), Study 2 (Count).
Supplemental_code/Integrative_Seurat ---> Seurat scRNA-seq integration pipeline for Study 1 (Count), Study 2 (TPM), Study 2 (Count).
Supplemental_code/unCTC ---> contain all analysis script for unCTC and markdown file to analyse Study 1 (Count), Study 2 (TPM), Study 2 (Count). 
Supplemental_code/Vanilla Seurat ---> Seurat standard clustering pipeline for Study 1 (Count), Study 2 (TPM), Study 2 (Count).
