DEGreport: Report of DEG analysis
Version 1.12.0

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.

AuthorLorena Pantano [aut, cre], John Hutchinson [ctb], Victor Barrera [ctb], Mary Piper [ctb]
Bioconductor views DifferentialExpression GeneExpression RNASeq ReportWriting Visualization
Date of publicationNone
MaintainerLorena Pantano <lorena.pantano@gmail.com>
LicenseMIT + file LICENSE
Version1.12.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DEGreport")

Getting started

README.md

Popular man pages

degCheckFactors: Distribution of gene ratios used to calculate Size Factors.
degComb: Get random combinations of two groups
degMB: Distribution of expression of DE genes compared to the...
degPlot: Plot top genes allowing more variables to color and shape...
degResults: Complete report from DESeq2 analysis
degVolcano: Create volcano plot from log2FC and adjusted pvalues data...
humanSexDEedgeR: DGEList object for DE genes betwen Male and Females
See all...

All man pages Function index File listing

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...
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...
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...
degPlotWide: Plot selected genes on a wide format
degPR: plot the correlation between the rank according estimator and...
degQC: Plot main figures showing p-values distribution 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

Functions

DEGreportSet Man page
convertIDs Source code
createReport Man page Source code
degBI Man page Source code
degBIcmd Man page Source code
degCheckFactors Man page Source code
degComb Man page Source code
degFC Man page Source code
degMB Man page Source code
degMV Man page Source code
degMean Man page Source code
degMerge Man page Source code
degNcomb Man page Source code
degObj Man page Source code
degPR Man page Source code
degPatterns Man page Source code
degPlot Man page Source code
degPlotWide Man page Source code
degQC Man page Source code
degRank Man page Source code
degResults Man page Source code
degVB Man page Source code
degVar Man page Source code
degVolcano Man page Source code
figurebyexp Source code
figurebyvar Source code
figurepvaluebyexp Source code
figurepvaluebyvar Source code
figurepvaluebyvarexp Source code
figurerank Source code
filter Source code
fmt Source code
geneInfo Man page
get_features Source code
group_metadata Source code
humanSexDEedgeR Man page
logger Source code
make_clusters Source code
mds Source code
median_per_cluster Source code
ntegrate Source code
plot_base Source code
plot_cluster Source code
reduce Source code
run_cluster_profiler Source code
save_file Source code
scale Source code
show_deseq2_results Man page
summarize_scale Source code
table_w_fc Source code
tablerank Source code

Files

.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
R
R/DEGreportSet.R
R/clustering.R
R/geneInfo.R
R/humanSexDEedgeR-data.R
R/methods.R
R/report.R
R/volcanoPlot.R
README.md
build
build/vignette.rds
data
data/DEGreportSet.rda
data/datalist
data/geneInfo.rda
data/humanSexDEedgeR.rda
inst
inst/NEWS
inst/doc
inst/doc/DEGreport.R
inst/doc/DEGreport.Rnw
inst/doc/DEGreport.pdf
inst/unitTests
inst/unitTests/test_singleFunctions.R
man
man/DEGreportSet.Rd
man/createReport.Rd
man/degBI.Rd
man/degBIcmd.Rd
man/degCheckFactors.Rd
man/degComb.Rd
man/degFC.Rd
man/degMB.Rd
man/degMV.Rd
man/degMean.Rd
man/degMerge.Rd
man/degNcomb.Rd
man/degObj.Rd
man/degPR.Rd
man/degPatterns.Rd
man/degPlot.Rd
man/degPlotWide.Rd
man/degQC.Rd
man/degRank.Rd
man/degResults.Rd
man/degVB.Rd
man/degVar.Rd
man/degVolcano.Rd
man/geneInfo.Rd
man/humanSexDEedgeR.Rd
tests
tests/runTests.R
vignettes
vignettes/DEGreport.Rnw
DEGreport documentation built on May 20, 2017, 10:17 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.