TCC

R package for tag count comparison

Differential expression analysis for tag count data with robust normalization strategies

This package provides functions for performing differential expression analysis using differentially expressed gene elimination strategy. A simple unified interface is provided which encapsulates functions to calculate normalization factors and estimate differentially expressed genes defined in edgeR, baySeq, and DESeq packages.
The appropriate combination provided by TCC allows a more robust and accurate estimation performed easily than directly using original packages. Functions to produce simulation data under various conditions and to plot the data are also provided.

Documentation

Documents of this software are available at http://www.iu.a.u-tokyo.ac.jp/~kadota/TCC/
in addition to the documents included in the software package.

Development versions

The development version is now on the github repository at https://github.com/tomoakin/TCC

Releases

Release of this software is made through CRAN at http://cran.r-project.org/web/packages/TCC/

No warranty

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Lisense

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License version 2 (GPL-2).

A copy of GPL-2 is accompanied in this directory in a file named COPYING.

Authors

Sun Jianqiang, Tomoaki Nishiyama, Kentaro Shimizu, and Koji Kadota