decode: Differential Co-Expression and Differential Expression Analysis
Version 1.2

Integrated differential expression (DE) and differential co-expression (DC) analysis on gene expression data based on DECODE (DifferEntial CO-expression and Differential Expression) algorithm.

AuthorThomas Lui [aut, cre]
Date of publication2015-07-14 20:40:34
MaintainerThomas Lui <tlui27@yahoo.com>
LicenseGPL-3
Version1.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("decode")

Getting started

Differential Co-Expression and Differential Expression Analysis"

Popular man pages

getAssoGeneSetPValue: Calculate the p-value between selected genes and functional...
getBonferroniPValue: Adjust p-value by Bonferroni correction
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
sumResult_MinGain: Summarize the functional gene set results into text file
See all...

All man pages Function index File listing

Man pages

getAssoGeneSetPValue: Calculate the p-value between selected genes and functional...
getBestAssociatedGeneSet: Get best associated functional gene sets for partitions of...
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...
sumResult_MinGain: Summarize the functional gene set results into text file

Functions

getAssoGeneSetPValue Man page Source code
getBestAssociatedGeneSet Man page Source code
getBonferroniPValue Man page Source code
getDE_DC_OptimalThreshold Man page Source code
getFDR Man page Source code
getPartitionIndex Man page Source code
getPathway Man page Source code
openFileToWrite Man page Source code
runDecode Man page Source code
sumResult_MinGain Man page Source code

Files

inst
inst/extdata
inst/extdata/geneSet.txt
inst/extdata/Expression_data_1400genes.txt
inst/extdata/Expression_data_50genes.txt
inst/doc
inst/doc/v.R
inst/doc/v.html
inst/doc/v.Rmd
NAMESPACE
R
R/sumResult_MinGain.r
R/getBonferroniPValue.r
R/getPathway.r
R/openFileToWrite.r
R/getAssoGeneSetPValue.r
R/getPartitionIndex.r
R/getFDR.r
R/Decode.r
R/getBestAssociatedGeneSet.r
R/getDE_DC_OptimalThreshold.r
vignettes
vignettes/v.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/getPathway.Rd
man/runDecode.Rd
man/getBonferroniPValue.Rd
man/getBestAssociatedGeneSet.Rd
man/openFileToWrite.Rd
man/sumResult_MinGain.Rd
man/getDE_DC_OptimalThreshold.Rd
man/getPartitionIndex.Rd
man/getFDR.Rd
man/getAssoGeneSetPValue.Rd
decode documentation built on May 20, 2017, 12:52 a.m.

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