Metadata-Version: 2.1
Name: allcools
Version: 0.1.6
Summary: Tool kit for single-cell methylome data analysis.
Home-page: https://github.com/lhqing/ALLCools
Author: Hanqing Liu
Author-email: hanliu@salk.edu
License: MIT
Description: # 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
        ![](/doc/file/ALLCools.svg)
        
        ## Get Start
        ### requirements
        ALLCools requires python > 3.6
        
        ### installation
        ```shell
        git clone https://github.com/lhqing/ALLCools.git
        cd ALLCools
        pip install .
        ```
        
        ### update
        ```shell
        # cd /path/to/ALLCools
        git pull
        pip install .
        ```
        
        ### use the ALLCools
        - CLI (recommand for non-python users)
        ```shell
        allcools -h
        allcools [FUNCTION_NAME] -h
        ```
        - API (recommand for integrating ALLCools with other python package, such as pybedtools, pybigwig, deeptools.)
        
        ```python
        from ALLCools.api import *
        ```
        
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Description-Content-Type: text/markdown
