Note
TCC remains available for reproducing existing workflows. For new DEGES-based normalization workflows, consider using normpatch.
normpatch provides a lightweight and extensible implementation of DEGES-based framework. It separates normalization from downstream differential expression testing and supports user-defined normalization and DEG-detection functions.
TCC 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 depended packages.