DMtools
latest

methylation

  • Getting started with dmtools
  • dmtools: command line tools
    • Process raw fastq data
    • Calculate DNA meth from bam
    • Format convertion
    • Estimate bs conversion rate
    • Calculate DNA meth with dm
      • Calculate DNA methylation for dm file
      • Calculate DNA methylation for regions
      • Calculate DNA methylation for gene body
      • Calculate methylation profile across genes
      • Calculate DNA methylation acorss chromosome
      • Calculate DNA methylation for chromosome
    • Merge or overlap dm files
    • Manipulate dm format
  • dmplot: plotting from the command line
  • dmdiff: differential dna methylation
  • Requirements
  • Python API: pydmtools
DMtools
  • Getting started
  • DMtools main modules
  • Edit on GitHub

DMtools main modules

You can view and process dm file with dmtools:

$ dmtools

obtained main modules in DMtools

  • Calculate DNA methylation for dm file
    • Description
    • Usage
    • Output
    • Parameters
  • Calculate DNA methylation for regions
    • Description
    • Usage and output
    • Parameters
  • Calculate DNA methylation for gene body
    • Description
    • Usage and output
    • Parameters
  • Calculate methylation profile across genes
    • Description
    • Usage
    • Parameters
  • Calculate DNA methylation acorss chromosome
    • Description
    • Usage
    • Parameters
  • Calculate DNA methylation for chromosome
    • Description
    • Usage
    • Parameters

Tip

For feature requests or bug reports please open an issue on github.

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