# TCC: Differential expression analysis for tag count data with robust normalization strategies

## Documentation for package ‘TCC’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

TCC-package | A package for differential expression analysis from tag count data with robust normalization strategies
arab | Arabidopsis RNA-Seq data set
calcAUCValue | Calculate AUC value from a TCC-class object
calcNormFactors | Calculate normalization factors
calcNormFactors-method | Calculate normalization factors
clusterSample | Perform hierarchical clustering for samples from expression data
do_TbT | Calculate normalization factors for raw tag count data using a multi-step normalization strategy called "TbT"
estimateDE | Estimate degrees of differential expression (DE) for individual genes
exactTestafterTbT | exactTest after TMM-baySeq-TMM procedure
filterLowCountGenes | Filter genes from a TCC-class object
getNormalizedData | Obtain normalized count data
getResult | Obtain the summaries of results after the differential expression analysis
hypoData | A simulation dataset for comparing two-group tag count data, focusing on RNA-seq
hypoData_mg | A simulation dataset for comparing three-group tag count data, focusing on RNA-seq
hypoData_ts | A sample microarray data for detecting tissue-specific patterns.
length | A container for storing information used in TCC
length-method | A container for storing information used in TCC
MAplot | plot a MA plot
nakai | DNA microarray data set
names | A container for storing information used in TCC
names-method | A container for storing information used in TCC
NBsample | Sampling from negative biomial distribution
plot | Plot a log fold-change versus log average expression (so-called M-A plot)
plot.TCC | Plot a log fold-change versus log average expression (so-called M-A plot)
plotFCPseudocolor | Create a pseudo-color image of simulation data
ROKU | detect tissue-specific (or tissue-selective) patterns from microarray data with many kinds of samples
show | A container for storing information used in TCC
show-method | A container for storing information used in TCC
show.TCC | A container for storing information used in TCC
simulateReadCounts | Generate simulation data from negative binomial (NB) distribution
subset | A container for storing information used in TCC
subset-method | A container for storing information used in TCC
TCC | A package for differential expression analysis from tag count data with robust normalization strategies
TCC-class | A container for storing information used in TCC
WAD | Calculate WAD statistic for individual genes
[ | A container for storing information used in TCC
[-method | A container for storing information used in TCC