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.