Ajaingithub/scmultiome_preprocessing

The automated single cell RNA and single cell ATAC preprocessing pipeline using Seurat and Signac.

scmultiome_preprocessing

The automated single cell RNA and single cell ATAC preprocessing pipeline using Seurat and Signac. This will also run ChromVar for Transcription factor enrichment

To Run the preprocessing of scmultiome

  source("scmultiome_Seurat_processing.R")
  savedir = "/research/labs/immunology/goronzy_weyand/GoronzyLab_Mayo/Abhinav/scmultiome/Huimin_and_DrGoronzy/final_seurat_obj/naive_resting/"
  
  rest_act <- readRDS("/research/labs/immunology/goronzy_weyand/GoronzyLab_Mayo/Abhinav/scmultiome/Huimin_and_DrGoronzy/final_seurat_obj/final_obj_res_act_old_young.RDS") # object should have Age
  rest_act@meta.data$Age <- gsub("#.*|#.*","",rownames(rest_act@meta.data))
  
  cellnames <- read.delim("/research/labs/immunology/goronzy_weyand/GoronzyLab_Mayo/Abhinav/scmultiome/Huimin_and_DrGoronzy/resting_cellnames.txt")
  
  scmultiome_pre(obj = rest_act,savedir = savedir, objname = "naive_resting", subset_cellnames = cellnames[,1])