CluBCpG: Cluster-Based analysis of CpG methylation
Whats new?
v0.3.0
- A major overhaul and modernization of the ClubCpG dependencies.
-
setup.py
removed in favor of apyproject.toml
- All project dependencies updated to modern versions
- Support of python 3.5, 3.6, 3.7, and 3.8 dropped
- Minimum version of python is now 3.9
- Added GitHub Actions workflows to automate testing of python 3.9 and 3.10
- Updated readthedocs build configuration ahead of deprecation of old method
What is CluBCpG?
CluBCpG is a software package built to analyze whole genome bisulfite sequencing (WGBS) data. This toolkit will divide each chromosome into small user-defined intervals, extract all WGBS reads within those intervals, cluster them based on identity, and write a final report to the use containing all identified CpG methylation patterns.
How do I use this?
Full documentation is available on ReadTheDocs
Requirements
- Python >= 3.9, <3.11
- Installation of Samtools on your PATH
Install
- (Optional, but HIGHLY recommended) Create a new python virtual environment and activate that virualenv
- Execute
pip install clubcpg
to install the package. Requirements will automatically be installed if not already present.
Developer Install
- Ensure all dependencies in
ubuntu-preinsatll.sh
are installed on the system. (Or equivilant packages if using fedora based system) - Install samtools, use
install-samtools.sh
- Make sure you have a compatible version of python installed
- Install Poetry
pip3 install poetry
- Run
poetry install
to install required packages and clubcpg - To install optional packages for docs building. Run
poetry install --with docs
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