# Differential Co-Expression and Differential Expression Analysis

## Documentation for package ‘decode’ version 1.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

getAssoGeneSetPValue | Calculate the p-value between selected genes and functional gene set
getBestAssociatedGeneSet | Get best associated functional gene sets for partitions of gene i
getBonferroniPValue | Adjust p-value by Bonferroni correction
getDE_DC_OptimalThreshold | Perform chi-square optimization
getFDR | Adjust p-value by Benjamini and Hochberg method
getPartitionIndex | Get gene index of 8 partitions for gene i
getPathway | read functional gene sets
openFileToWrite | Open file to write result
runDecode | Differential Co-Expression and Differential Expression Analysis
sumResult_MinGain | Summarize the functional gene set results into text file