ALLCools: ALL methyl-Cytosine tools

ALLCools: ALL methyl-Cytosine tools

ALLCools is a software package for single-cell DNA methylome data analysis. It contains functions for cellular and genomic analysis.

Documentation Organization

  1. For installation, please read GET STARTED here;

  2. The ALLCools workflow encompasses the following two sections:

    1. CELLULAR ANALYSIS: This section goes over basic clustering steps, differential methylated genes (DMG) analysis, data integration, and doublets identification;

    2. GENOMIC ANALYSIS: This section covers differential methylated region (DMR) calling, genome annotation, DNA motif analysis, correlation analysis, and enhancer prediction;

  3. To generate analysis files from your own data, please read the COMMAND LINE TOOLS here;

  4. For references to function used in this package, please read the API here.


Fig. 1 ALLCools documentation organization.


  • Hanqing Liu, developer, initial conception

  • Jingtian Zhou, developer, 5kb clustering algorithms

  • Wei Tian

  • Jiaying Xu



Fig. 2 Click on this to create a page specific issue.

  • The source code is on github;

  • For releases and changelog, please check out the github releases page;

  • For bugs and feature requests, please use the issue tracker.

  • For page-specific issues, please use the “open issue” button on the top-right toggle.

Citing ALLCools

If ALLCools has been significant in your research, and you would like to acknowledge the project in your academic publication, we suggest citing our paper [Liu et al., 2021]. For any specific methods and algorithms, also consider citing the original author’s paper included in the Citation and Reference page here.