CompGO: An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation

This package contains functions to accomplish several tasks. It is able to download full genome databases from UCSC, import .bed files easily, annotate these .bed file regions with genes (plus distance) from aforementioned database dumps, interface with DAVID to create functional annotation and gene ontology enrichment charts based on gene lists (such as those generated from input .bed files) and finally visualise and compare these enrichments using either directed acyclic graphs or scatterplots.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CompGO")
AuthorSam D. Bassett [aut], Ashley J. Waardenberg [aut, cre]
Bioconductor views GO GeneSetEnrichment MultipleComparison Visualization
Date of publicationNone
MaintainerAshley J. Waardenberg <A.Waardenberg@victorchang.edu.au>
LicenseGPL-2
Version1.12.0

View on Bioconductor

Files

.Rinstignore
DESCRIPTION
NAMESPACE
NEWS
R
R/fullPipeline.R
build
build/vignette.rds
data
data/bed.sample.txt
data/bed.sample.txt.gz
data/gata4.txt
data/mef2a.txt
data/nkx25.txt
data/p300.txt
data/srf.txt
data/tbx5.txt
inst
inst/doc
inst/doc/CompGO-Intro.R
inst/doc/CompGO-Intro.Rnw
inst/doc/CompGO-Intro.pdf
man
man/PCAplot.Rd man/annotateBedFromDb.Rd man/bed.sample.Rd man/compareZscores.Rd man/doZtrans.single.Rd
man/gata4.rd
man/getFnAnot_genome.Rd
man/mef2a.rd
man/nkx25.rd
man/p300.rd
man/plotDendrogram.Rd man/plotInteractive.Rd man/plotPairwise.Rd man/plotTwoGODags.Rd man/plotZRankedDAG.Rd man/plotZScores.Rd man/slidingJaccard.Rd
man/srf.rd
man/tbx5.rd
man/viewKegg.Rd man/zTransformDirectory.Rd
vignettes
vignettes/CompGO-Intro.Rnw

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

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

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