ROKU
(Package: TCC) :
detect tissue-specific (or tissue-selective) patterns from
ROKU is a method for detecting tissue-specific (or tissue-selective) patterns from gene expression data for many tissues (or samples). ROKU (i) ranks genes according to their overall tissue-specificity using Shannon entropy after data processing and (ii) detects tissues specific to each gene if any exist using an Akaike's information criterion (AIC) procedure.
● Data Source:
BioConductor
● Keywords:
● Alias: ROKU
●
0 images
TCC-class
(Package: TCC) :
A container for storing information used in TCC
This is a container class for TCC. This class initially contains count data matrix and some information for the analysis of count data. It also provides further fields that are populated during the analysis.
TCC
(Package: TCC) :
A package for differential expression analysis from tag
This package performs differential expression analysis from transcriptome data that are produced from high-throughput sequencing (HTS) and microarray technologies. A notable feature of this package is to provide robust normalization methods whose strategy is to remove data assigned as potential differentially expressed genes (DEGs) before performing normalization for RNA-seq count data (Kadota et al., 2012; Sun et al., 2013).
WAD
(Package: TCC) :
Calculate WAD statistic for individual genes
This function performs WAD method to identify differentially expressed genes (DEGs) from two-group gene expression data. A high absolute value for the WAD statistic is evident of a high degree of differential expression.
This function calculates normalization factors using a specified multi-step normalization method from a TCC-class object. The procedure can generally be described as the STEP1-(STEP2-STEP3)n pipeline.
estimateDE
(Package: TCC) :
Estimate degrees of differential expression (DE) for individual genes
This function calculates p-values (or the related statistics) for identifying differentially expressed genes (DEGs) from a TCC-class object. estimateDE internally calls a specified method implemented in other R packages.
This function takes a TCC object and returns a new TCC object without genes having low count tags across samples. The threshold is configurable with low.count parameter.
providing 
.