wgmao / ALLCools

Tool kit for ALLC format and methylation analysis

ALLCools

• 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 Function Map

Get Start

requirements

ALLCools requires python > 3.6

installation

git clone https://github.com/lhqing/ALLCools.git
cd ALLCools
pip install .

update

# cd /path/to/ALLCools
git pull
pip install .

use the ALLCools

• 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 *