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

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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.

Author
Sam D. Bassett [aut], Ashley J. Waardenberg [aut, cre]
Date of publication
None
Maintainer
Ashley J. Waardenberg <A.Waardenberg@victorchang.edu.au>
License
GPL-2
Version
1.10.0

View on Bioconductor

Man pages

annotateBedFromDb
Annotate .bed file to genes
bed.sample
A sample of 25 rows from a .bed file of mm9 regions
compareZscores
Compare the Z scores of individual GO terms between two input...
doZtrans.single
Z transform a single functional annotation chart from DAVID
getFnAnot_genome
Get the functional annotation chart of a gene list using...
PCAplot
Plot PCA given an input list of fnAnot charts
plotDendrogram
Plot dendrogram given an input list of fnAnot charts
plotInteractive
Interactive plotting function for groups of GO terms
plotPairwise
Generates a scatterplot of two sets of GO terms based on...
plotTwoGODags
Plots a directed acyclic graph of GO terms from two different...
plotZRankedDAG
Plot a directed acyclic graph (DAG) based on the corrected...
plotZScores
Performs z transform on two sets of GO terms and plots...
slidingJaccard
Plot two functional annotation charts using a sliding Jaccard...
viewKegg
Compare KEGG pathways between two functional annotation...
zTransformDirectory
Z-score transformation of DAVID functional annotation charts...

Files in this package

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