/RA3

RA3 method for integrative analysis of single cell ATAC sequence data.

Primary LanguageRGNU Lesser General Public License v3.0LGPL-3.0

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:
    1. Use TF-IDF for matrix normailization,
    2. 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.