Detection of differential binding events in ChIP-seq data is still a tricky business. For a new collaboration, the whole project is going to depend on it, so I went out there and tried to collect existing tools, work with them and see their pros and cons.

I was looking specifically for tools that work well without replicates or input controls since we already have some data lying around from a pilot in the begging of the project, but they might be useful as well as the data comes along.

In no particular order:


  • Robust tutorial.
  • Requires a strict table with sample annotation (not necessarily bad though).
  • Requires peak files.
  • Uses multiple replicates in analysis.
  • Always requires input files to perform analysis.
  • Close R integration provides many useful methods to explore output by plotting.


  • Requires peak files.
  • Does not require input files.
  • Terrible code packaging and usage practices.

Commands to install dependencies are outdated. If anyone is also strugling with it, here’s what worked for me:



  • Installation is not straightforward (dependency hell).
  • Requires peak files.
  • Does not require input files (but can be used for fold enrichment filtering).
  • Some nice tools downstream of differential calling (mostly region annotation).


  • Can use inputs for analysis.
  • Limited description of output.
  • Output in “a proprietary BED format” (do I need to say anything?)


  • Does not require peak files.
  • Poor documentation on the diff bind functions
  • Very immature code (“prepare a pen to write down the number of non-redundant reads” - seriously?)



  • Requires more than one replicate per condition for analysis.
  • Does not require peak files.
  • Does not require input files.
  • Supports several input file formats.


  • No documentation besides a readme in a zip file.
  • Not really packaged.


  • Poor documentation (only function description in the R package).


  • Useful tutorial.
  • Only recommended for point-source factors.
  • Requires peak files.
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