RefTM

R package for RefTM. Stochastic variational inference method is used to fit LDA models.

Install

install.packages("devtools")
devtools::install_github("cuhklinlab/RefTM")

Functions

This package includes following main functions:

• RefTM runs RefTM for the analysis of single-cell chromatin accessibility sequencing data.
• RefTM_postprocess postprocess the result to obtain a final cell-by-topic matrix as the output of RefTM.
• RefTM_motif runs motif enrichment based on the output of RefTM.

Documentation

Please check the vigenette for a detailed tutorial.