Package: TCC
Type: Package
Title: TCC: Differential expression analysis for tag count data with
        robust normalization strategies
Version: 1.2.0
Author: Jianqiang Sun, Tomoaki Nishiyama, Kentaro Shimizu, and Koji Kadota
Maintainer: Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp>, Tomoaki
        Nishiyama <tomoakin@staff.kanazawa-u.ac.jp>
Description: This package provides a series of functions for performing
    differential expression analysis from RNA-seq count data using robust
    normalization strategy (called DEGES). The basic idea of DEGES is that
    potential differentially expressed genes or transcripts (DEGs) among
    compared samples should be removed before data normalization to obtain
    a well-ranked gene list where true DEGs are top-ranked and non-DEGs are
    bottom ranked. This can be done by performing a multi-step normalization
    strategy (called DEGES for DEG elimination strategy). A major
    characteristic of TCC is to provide the robust normalization methods for
    several kinds of count data (two-group with or without replicates, 
    multi-group/multi-factor, and so on) by virtue of the use of combinations
    of functions in other sophisticated packages (especially edgeR, DESeq, 
    and baySeq).
Depends: R (>= 2.15), methods, DESeq, edgeR, baySeq, ROC
Imports: EBSeq, samr
Suggests: RUnit, BiocGenerics
Enhances: snow
biocViews: HighThroughputSequencing, DifferentialExpression, RNAseq
License: GPL-2
Copyright: Authors listed above
Packaged: 2013-10-15 08:31:41 UTC; biocbuild
Built: R 3.0.2; ; 2013-10-15 16:13:43 UTC; windows
