This repository contains code for in vivo peturb-seq.
The main code directory is CodeDirectory_Current, and particularly the RunPipeline.sh code that runs most analysis from the paper automatically.
By subdirectory:
10X_Perturb_Code: code for extracting perturb-seq perturbation information from 10X single cell data
DialoutCode: code for extracting perturb-seq perturbation information from dialout reads and making them in a nice format
Dialout_Results: downstream code to clean up the dialout results
DECode: Code to perform DE analysis (with limma) on the perturb-seq data. Not included in the RunPipeline.sh script
SeuratObjects: Scripts that go from the raw count matrices to a final Seurat object with the perturb-seq data
CompareToHuman: The code that looks for how the WGCNA modules we found are conserved in various human datasets. Not run in that standard pipeline
UpdateSTM: Runs code to parse strucutural topic model topics run on the Perturb-seq data for publication
CellComposition: Code for comparing cell type composition between perturbations