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 |