| 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 |