| All functions | 
      
        
        | DEGSet()DEGSet()as.DEGSet()
 | DEGSet | 
        
        | DEGreport-package
 | Deprecated functions in package DEGreport | 
        
        | createReport()
 | Create report of RNAseq DEG anlaysis | 
        
        | deg()
 | Method to get all table stored for an specific comparison | 
        
        | degCheckFactors()
 | Distribution of gene ratios used to calculate Size Factors. | 
        
        | degColors()
 | Make nice colors for metadata | 
        
        | degComps()
 | Automatize the use of results()for multiple comparisons | 
        
        | degCorCov()
 | Calculate the correlation relationshipt among all covariates
in the metadata table | 
        
        | degCovariates()
 | Find correlation between pcs and covariates | 
        
        | degDefault()degCorrect()
 | Method to get the default table to use. | 
        
        | degFilter()
 | Filter genes by group | 
        
        | degMA()
 | MA-plot from base means and log fold changes | 
        
        | degMB()
 | Distribution of expression of DE genes compared to the background | 
        
        | degMDS()
 | Plot MDS from normalized count data | 
        
        | degMV()
 | Correlation of the standard desviation and the mean of the abundance of a
set of genes. | 
        
        | degMean()
 | Distribution of pvalues by expression range | 
        
        | degMerge()
 | Integrate data comming from degPattern into one data object | 
        
        | degObj()
 | Create a deg object that can be used to plot expression values
at shiny server:runGist(9930881) | 
        
        | degPCA()
 | smart PCA from count matrix data | 
        
        | degPatterns()
 | Make groups of genes using expression profile. | 
        
        | degPlot()
 | Plot top genes allowing more variables to color and shape points | 
        
        | degPlotCluster()
 | Plot clusters from degPattern function output | 
        
        | degPlotWide()
 | Plot selected genes on a wide format | 
        
        | degQC()
 | Plot main figures showing p-values distribution and mean-variance correlation | 
        
        | degResults()
 | Complete report from DESeq2 analysis | 
        
        | degSignature()
 | Plot gene signature for each group and signature | 
        
        | degSummary()
 | Print Summary Statistics of Alpha Level Cutoffs | 
        
        | degVB()
 | Distribution of the standard desviation of
DE genes compared to the background | 
        
        | degVar()
 | Distribution of pvalues by standard desviation range | 
        
        | degVolcano()
 | Create volcano plot from log2FC and adjusted pvalues data frame | 
        
        | geneInfo
 | data.frame with chromose information for each gene | 
        
        | geom_cor()
 | Add correlation and p-value to a ggplot2 plot | 
        
        | humanGender
 | DGEList object for DE genes betwen Male and Females | 
        
        | significants()
 | Method to get the significant genes |