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ChIP-SEQ Statistical Power CSSP

A statistical framework for power calculations in ChIP-seq experiments by considering a local Poisson model, which is commonly adopted by many peak callers. Evaluations with simulations and data-driven computational experiments demonstrate that CSSP (ChIP-seq Statistical Power) can reliably estimate the power of a ChIP-seq experiment at different sequencing depths based on pilot data. Furthermore, it provides an analytical approach for calculating the required depth for a targeted power while controlling the false discovery rate at a user-specified level. Our results enable researchers to use their own or publicly available data for determining required sequencing depths of their ChIP-seq experiments and potentially make better use of the multiplexing functionality of the sequencers.

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CSSP forum

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CSSP classification

CSSP specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 2.0
Stability:
Stable

CSSP distribution

versioning

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No versioning.

CSSP support

Documentation

Credits

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Publications

Institution(s)

Department of Statistics, and Department of Biostatistics and Medical Informatics, Madison, USA

Link to literature

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