createReport |
Create report of RNAseq DEG anlaysis |
degBI |
Get the estimates of the fold change (FC) mean from a FC distribution using bayesian inference |
degBIcmd |
Apply bayesian inference to estimate the average fold change (FC) of a distribution |
degCheckFactors |
Distribution of gene ratios used to calculate Size Factors. |
degComb |
Get random combinations of two groups |
degFC |
get the FC for each gene between two groups |
degMB |
Distribution of expression of DE genes compared to the background |
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. |
degNcomb |
Get number of potential combinations of two vectors |
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 |
degPlot |
Plot top genes allowing more variables to color and shape points |
degPlotWide |
Plot selected genes on a wide format |
degPR |
plot the correlation between the rank according estimator and the rank according FC |
degQC |
Plot main figures showing p-values distribution and mean-variance correlation |
degRank |
Get rank data frame with best score on the top |
DEGreportSet |
List of process geuvadis data to test the package |
degResults |
Complete report from DESeq2 analysis |
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 |
geneInfo |
data.frame with chromose information for each gene |
humanSexDEedgeR |
DGEList object for DE genes betwen Male and Females |
show_deseq2_results |
Complete report from DESeq2 analysis |