Getting started

What is PRISM?

Note

This section is under construction.

How PRISM works

Note

This section is under construction

Installation

Note

This section is under construction.

Installing via pip

PRISM is distributed as a python package named subclone-prism, so it can be easily installed via PyPI.

$ pip install subclone-prism

Installing via bioconda

PRISM will support installation via bioconda soon.

Installing from source

The latest version of PRISM can be installed by directly cloning the github repository.

$ git clone https://github.com/dohlee/prism.git
$ cd prism
$ python setup.py install

Requirements

Note

This section is under construction.

PRISM requires BAM file of RRBS reads, aligned by Bismark.

PRISM strictly requires mapping results of Bismark, a bisulfite read mapping tool. Also note that PRISM only applies to RRBS data, and unfortunately, the feasibility of PRISM to the data from other methylation profiling techniques such as whole genome bisulfite sequencing (WGBS), methylated DNA immunoprecipitation sequencing (MeDIP-Seq), or methyl-CpG binding domain-based capture sequencing (MBDCap-Seq) has not been verified.