All functions
|
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. |
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
|
Method to get the default table to use. |
degFilter
|
Filter genes by group |
degMB
|
Distribution of expression of DE genes compared to the background |
degMDS
|
Plot MDS from normalized count data |
degMean
|
Distribution of pvalues by expression range |
degMerge
|
Integrate data comming from degPattern into one data object |
degMV
|
Correlation of the standard desviation and the mean of the abundance of a
set of genes. |
degObj
|
Create a deg object that can be used to plot expression values
at shiny server:runGist(9930881) |
degPatterns
|
Make groups of genes using expression profile |
degPCA
|
smart PCA from count matrix data |
degPlot
|
Plot top genes allowing more variables to color and shape points |
degPlotWide
|
Plot selected genes on a wide format |
degQC
|
Plot main figures showing p-values distribution and mean-variance correlation |
DEGreport-package
|
Deprecated functions in package DEGreport |
degResults
|
Complete report from DESeq2 analysis |
DEGSet DEGSetFromEdgeR DEGSetFromDESeq2
|
DEGSet |
degSummary
|
Print Summary Statistics of Alpha Level Cutoffs |
degVar
|
Distribution of pvalues by standard desviation range |
degVB
|
Distribution of the standard desviation of
DE genes compared to the background |
degVolcano
|
Create volcano plot from log2FC and adjusted pvalues data frame |
colors
|
data.frame with chromose information for each gene |
humanGender
|
DGEList object for DE genes betwen Male and Females |
plotMA
|
MA-plot from base means and log fold changes |
significants
|
Method to get the significant genes |