- A toolkit for ALLC format and bulk/single-cell methylation sequencing analysis.
- It provides all necessary functions about generating, manipulating and transfering 2 file formats:
- the ALLC format, a tab-sparated text format storing base-level raw methylation information for 1 sample.
- the MCDS format, a integrated HDF5 dataset storing region-level raw methylation information for a group of samples/cells.
- This package is still under active development
ALLCools requires python > 3.6
git clone https://github.com/lhqing/ALLCools.git
cd ALLCools
pip install .
# cd /path/to/ALLCools
git pull
pip install .
- CLI (recommand for non-python users)
allcools -h
allcools [FUNCTION_NAME] -h
- API (recommand for integrating ALLCools with other python package, such as pybedtools, pybigwig, deeptools.)
from ALLCools.api import *