YAME - Understand Sequencing Level Methylation Data

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YAME (Yet Another MEthylation tool) is a methylation toolset designed for sequence-level DNA methylation data management. It is a command-line C program capable of performing sequence-level enrichment testing, row operations (such as merging pseudobulks), downsampling, and other related tasks with ultra fast speed.

Reference

David Goldberg, Hongxiang Fu, et al., KnowYourCG: supervised learning of sparse DNA methylomes, Manuscript in submission

Installation Guide

The source can be retrieved by:

# git
git clone https://github.com/zhou-lab/YAME.git
cd YAME

After retrieving the source code, building YAME simply proceeds as follows:

make

If you want to run yame from anywhere without specifying the path, move it to a directory that is already in your PATH, such as ~/bin

mv ./yame ~/bin/yame

Overview of Functionalities

The following list provides an overview of the various functionalities provided by YAME. You can also find much of this by typing YAME in the terminal after installation.

  • pack Pack data into a cx file.
  • unpack Unpack data from a cx file.
  • subset Subset samples from a cx file.
  • rowsub Subset rows a cx file using an index list file.
  • info Display basic parameter of the cx file.
  • summary calculate summary, with or without masks.
  • index Index samples in a cx file.
  • split Split multi-sample data into single-sample data.
  • chunk Chunk data into smaller fragments.
  • chunkchar Chunk text data into smaller fragments.
  • rowop Perform operations on rows, e.g., sum binary values.
  • mask Mask methylation data by setting masked record to M=U=0.
  • dsample Downsample methylation data by setting unsampled records to M=U=0.

Acknowledgement

  • This work is supported by NIH/NIGMS 5R35GM146978.