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.

AuthorSam D. Bassett [aut], Ashley J. Waardenberg [aut, cre]
Date of publicationNone
MaintainerAshley J. Waardenberg <A.Waardenberg@victorchang.edu.au>
LicenseGPL-2
Version1.10.0

View on Bioconductor

Files

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

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.