Decomposition-based peak identification, which find peaks across a large number of TSS (transcription starting site) profiles
Ruby R Shell
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Failed to load latest commit information.

Decomposition-based peak identification (DPI)

This tool identifies a set of reference peaks in in genome-wide TSS (transcription starting site) profiles obtained from diverse range of biological states. In particular, this is developed for the FANTOM5 project (Nature 507, 462-467, 2014 and its related papers) that produced CAGE profiles in more than one thousand of biological states in human and mouse, and the analysis results have been available at as well as the article above.

In general, I recommend to use the FANTOM5 peak set for CAGE analysis, rather than runnning this tool for your own data, so that you can compare your results with others. I would recommend to run this tool to identify a set of TSS peaks in other organisms than human and mouse, or very unique biological conditions not included in the FANTOM5 sample collecttion.



% git clone

How to run

% ./ [options]

Follow the usage described in the message.

Update (branches)

  • beta3 (current master) (Aug, 2018)
    • updated for platform compatibility
  • beta2 (June, 2016)
    • updated for compatibility to the recent version of bedtools (v2.25.0) and jksrc (v333).
    • updated for portability of user environment
  • beta (Sep, 2014)
    • a wrapper script is updated as '', enabling to run the steps in any directory.
    • set 'non-decomposition' mode as default
  • alpha (April, 2014)
    • a wrapper script '' perform all the requried steps.
  • core (Dec, 2013):
    • only the core script of R


Hideya Kawaji


2014-2017 RIKEN, Japan.


  • A promoter level mammalian expression atlas, Forrest A, Kawaji H, Rehli M, et al. Nature 507, 462-467, 2014