DEGreport: Report of DEG analysis

Creation of a HTML report of differential expression analyses of count data. It integrates some of the code mentioned in DESeq2 and edgeR vignettes, and report a ranked list of genes according to the fold changes mean and variability for each selected gene.

Author
Lorena Pantano
Date of publication
None
Maintainer
Lorena Pantano <lorena.pantano@gmail.com>
License
MIT + file LICENSE
Version
1.10.0

View on Bioconductor

Man pages

createReport
Create report of RNAseq DEG anlaysis
degBI
Get the estimates of the fold change (FC) mean from a FC...
degBIcmd
Apply bayesian inference to estimate the average fold change...
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...
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...
degNcomb
Get number of potential combinations of two vectors
degObj
Create a deg object that can be used to plot expression...
degPatterns
Make groups of genes using expression profile
degPlot
Plot top genes allowing more variables to color and shape...
degPR
plot the correlation between the rank according estimator and...
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...
degVolcano
Create volcano plot from log2FC and adjusted pvalues data...
geneInfo
data.frame with chromose information for each gene
humanSexDEedgeR
DGEList object for DE genes betwen Male and Females

Files in this package

DEGreport/.travis.yml
DEGreport/DESCRIPTION
DEGreport/LICENSE
DEGreport/NAMESPACE
DEGreport/R
DEGreport/R/DEGreportSet.R
DEGreport/R/clustering.R
DEGreport/R/geneInfo.R
DEGreport/R/humanSexDEedgeR-data.R
DEGreport/R/methods.R
DEGreport/R/report.R
DEGreport/R/volcanoPlot.R
DEGreport/README.md
DEGreport/build
DEGreport/build/vignette.rds
DEGreport/data
DEGreport/data/DEGreportSet.rda
DEGreport/data/datalist
DEGreport/data/geneInfo.rda
DEGreport/data/humanSexDEedgeR.rda
DEGreport/inst
DEGreport/inst/NEWS
DEGreport/inst/doc
DEGreport/inst/doc/DEGreport.R
DEGreport/inst/doc/DEGreport.Rnw
DEGreport/inst/doc/DEGreport.pdf
DEGreport/inst/unitTests
DEGreport/inst/unitTests/test_singleFunctions.R
DEGreport/man
DEGreport/man/DEGreportSet.Rd
DEGreport/man/createReport.Rd
DEGreport/man/degBI.Rd
DEGreport/man/degBIcmd.Rd
DEGreport/man/degComb.Rd
DEGreport/man/degFC.Rd
DEGreport/man/degMB.Rd
DEGreport/man/degMV.Rd
DEGreport/man/degMean.Rd
DEGreport/man/degMerge.Rd
DEGreport/man/degNcomb.Rd
DEGreport/man/degObj.Rd
DEGreport/man/degPR.Rd
DEGreport/man/degPatterns.Rd
DEGreport/man/degPlot.Rd
DEGreport/man/degRank.Rd
DEGreport/man/degResults.Rd
DEGreport/man/degVB.Rd
DEGreport/man/degVar.Rd
DEGreport/man/degVolcano.Rd
DEGreport/man/geneInfo.Rd
DEGreport/man/humanSexDEedgeR.Rd
DEGreport/tests
DEGreport/tests/runTests.R
DEGreport/vignettes
DEGreport/vignettes/DEGreport.Rnw