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Fast and efficient summarization of generic bedGraph files from single cell bisufite sequencing

THIS PACKAGE IS STILL UNDER DEVELOPMENT. CONTENT INCLUDED HERE MAY NOT REFLECT THE CURRENT STATE OF THE PACKAGE.

Introduction

scMethrix provides set of function which allows easy importing of various flavors of bedgraphs generated by methylation callers, and many downstream analysis to be performed on large matrices.

This vignette describes basic usage of the package intended to process several large bedgraph files in R. In addition, a detailed exemplary complete data analysis with steps from reading in to annotation and differential methylation calling can be found in our WGBS best practices workflow

Installation

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

#Installing developmental version from GitHub
BiocManager::install("CompEpigen/scMethrix")

NOTE

Installation from BioConductor requires the BioC and R versions to be the newest. This arises from the restrictions imposed by BioConductor community which might cause package incompatibilities with the earlier versions of R (for e.g; R < 4.0). In that case installing from GitHub might be easier since it is much more merciful with regards to versions.

Basic Overview