data_processing: A function to process the h5 file from CellBender and...
In HaojiaWu/plot1cell: A package for single cell data visualization

data_processing

R Documentation

A function to process the h5 file from CellBender and generate QC plots

Description

This function works only with the h5 file output from CellBender. It takes the count table, clusters the cells, removes the doublets (DoubletFinder), and recluster the cells, and finally output a Seurat object

Usage

data_processing(cellbender_h5, sampleID, out_dir, species, type)

Arguments

`cellbender_h5`	The h5 file from CellBender output
`sampleID`	ID given to the run
`out_dir`	Output directory
`species`	It can be "human" or "mouse"
`type`	It can be "cell" or "nucleus". If your data is from snRNA-seq, use "type = nucleus". Otherwise, use "type = cell".