Single cell RNA-seq analysis pipeline.
This repo has a collection of scripts to process scRNA-seq data. There is a kallisto-bustools version and a CellRanger pipeline for primary data processing.
kallisto-bustools processes reads only to the annotated exons of the genes.
CellRanger processes reads to the introns as well as the exons by default. Exon only analysis can be specified in the options.
Scripts for import of both primary analysis pipelines into R for creation of a Seurat object are located in the pipelines respective directory.
The src directory contains scripts for further processing the Seurat object.
DecontX removes ambiant RNA contamination.
DoubletFinder performs automated detection of heterotypic doublets.
SCT v2 is used for normalization.
scType is used for cell type annotation.
The annotation directory contains cell type annotation lists for running with scType.