TCC: an R package for comparing tag count data with robust normalization strategies.

ABSTRACT:

Background

Differential expression analysis based on "next-generation" sequencing technologies is a fundamental means of studying RNA expression. We recently developed a multi-step normalization method (called TbT) for two-group RNA-seq data with replicates and demonstrated that the statistical methods available in four R packages (edgeR, DESeq, baySeq, and NBPSeq) together with TbT can produce a well-ranked gene list in which true differentially expressed genes (DEGs) are top-ranked and non-DEGs are bottom ranked. However, the advantages of the current TbT method come at the cost of a huge computation time. Moreover, the R packages did not have normalization methods based on such a multi-step strategy.

Results

TCC (an acronym for Tag Count Comparison) is an R package that p

SUBMITTER: Sun J 

PROVIDER: S-EPMC3716788 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature