RA3
RA3 method for integrative analysis of single cell ATAC sequence data.
Installation
You can install the released version of package Ra3 from Github:
devtools::install_github("cuhklinlab/RA3")
Main funcitons
This package includes following functions:
runRA3
Run RA3 for integrative analysis of scATAC-seq data.Dataprep
Normalize count matrix. This funciton is optional for normalization of runRA3's input count matrix. It consists of two steps:- Use TF-IDF for matrix normailization,
- Select peaks for rough dimension reduction.
RA3_EM
EM algorithm for RA3. This function is implementing an EM algorithm to estimate parameters of RA3 model.
Tutorial
Please check the vigenette for a tutorial. Two examples are contained for a quick start of RA3.