decode: Differential Co-Expression and Differential Expression Analysis

Share:

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

Author
Thomas Lui [aut, cre]
Date of publication
2015-07-14 20:40:34
Maintainer
Thomas Lui <tlui27@yahoo.com>
License
GPL-3
Version
1.2

View on CRAN

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

Files in this package

decode
decode/inst
decode/inst/extdata
decode/inst/extdata/geneSet.txt
decode/inst/extdata/Expression_data_1400genes.txt
decode/inst/extdata/Expression_data_50genes.txt
decode/inst/doc
decode/inst/doc/v.R
decode/inst/doc/v.html
decode/inst/doc/v.Rmd
decode/NAMESPACE
decode/R
decode/R/sumResult_MinGain.r
decode/R/getBonferroniPValue.r
decode/R/getPathway.r
decode/R/openFileToWrite.r
decode/R/getAssoGeneSetPValue.r
decode/R/getPartitionIndex.r
decode/R/getFDR.r
decode/R/Decode.r
decode/R/getBestAssociatedGeneSet.r
decode/R/getDE_DC_OptimalThreshold.r
decode/vignettes
decode/vignettes/v.Rmd
decode/MD5
decode/build
decode/build/vignette.rds
decode/DESCRIPTION
decode/man
decode/man/getPathway.Rd
decode/man/runDecode.Rd
decode/man/getBonferroniPValue.Rd
decode/man/getBestAssociatedGeneSet.Rd
decode/man/openFileToWrite.Rd
decode/man/sumResult_MinGain.Rd
decode/man/getDE_DC_OptimalThreshold.Rd
decode/man/getPartitionIndex.Rd
decode/man/getFDR.Rd
decode/man/getAssoGeneSetPValue.Rd