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


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Documentation for package ‘TCC’ version 1.47.0

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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