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

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Documentation for package ‘TCC’ version 1.47.0

• 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
estimateDE	Estimate degrees of differential expression (DE) for individual genes
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
makeFCMatrix	Generate the fold change matrix for simulating count data
nakai	DNA microarray data set
names	A container for storing information used in TCC
names-method	A container for storing information used in TCC
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