geneListPie: Profiling a gene list into GOslim or KEGG function pie

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"geneListPie" package is for mapping a gene list to function categories defined in GOSlim or Kegg. The results can be plotted as a pie chart to provide a quick view of the genes distribution of the gene list among the function categories. The gene list must contain a list of gene symbols. The package contains a set of pre-processed gene sets obtained from Gene Ontology and MSigDB including human, mouse, rat and yeast. To provide a high level concise view, only GO slim and kegg are provided. The gene sets are regulared updated. User can also use customized gene sets. User can use the R Pie() or Pie3D() function for plotting the pie chart. Users can also choose to output the gene function mapping results and use external software such as Excel(R) for ploting.

Author
Xutao Deng
Date of publication
2012-07-23 10:35:32
Maintainer
Xutao Deng <xutaodeng@gmail.com>
License
GPL-3
Version
1.0

View on CRAN

Man pages

geneListPie-package
Profiling a gene list into GOslim or KEGG function pie
geneListProfile
Profling a gene list against gene sets
goslim.human.all
goslim.human.all
goslim.human.BP
goslim.human.BP
goslim.human.CC
goslim.human.CC
goslim.human.MF
goslim.human.MF
goslim.mouse.all
goslim.mouse.all
goslim.mouse.BP
goslim.mouse.BP
goslim.mouse.CC
goslim.mouse.CC
goslim.mouse.MF
goslim.mouse.MF
goslim.rat.all
goslim.rat.all
goslim.rat.BP
goslim.rat.BP
goslim.rat.CC
goslim.rat.CC
goslim.rat.MF
goslim.rat.MF
goslim.yeast.all
goslim.yeast.all
goslim.yeast.BP
goslim.yeast.BP
goslim.yeast.CC
goslim.yeast.CC
goslim.yeast.MF
goslim.yeast.MF
kegg2.5.generic
kegg2.5.generic
load.genelist
load a gene list into workspace
load.genesets
Load customized gene sets into work space
printGeneListProfile
Print the profiling results

Files in this package

geneListPie
geneListPie/MD5
geneListPie/R
geneListPie/R/geneListPie.R
geneListPie/man
geneListPie/man/goslim.rat.BP.Rd
geneListPie/man/goslim.mouse.BP.Rd
geneListPie/man/goslim.human.all.Rd
geneListPie/man/geneListProfile.Rd
geneListPie/man/goslim.mouse.all.Rd
geneListPie/man/load.genesets.Rd
geneListPie/man/kegg2.5.generic.Rd
geneListPie/man/goslim.mouse.MF.Rd
geneListPie/man/goslim.yeast.BP.Rd
geneListPie/man/printGeneListProfile.Rd
geneListPie/man/goslim.human.CC.Rd
geneListPie/man/goslim.yeast.MF.Rd
geneListPie/man/goslim.rat.CC.Rd
geneListPie/man/goslim.rat.all.Rd
geneListPie/man/goslim.yeast.all.Rd
geneListPie/man/geneListPie-package.Rd
geneListPie/man/load.genelist.Rd
geneListPie/man/goslim.mouse.CC.Rd
geneListPie/man/goslim.human.BP.Rd
geneListPie/man/goslim.rat.MF.Rd
geneListPie/man/goslim.human.MF.Rd
geneListPie/man/goslim.yeast.CC.Rd
geneListPie/NAMESPACE
geneListPie/DESCRIPTION
geneListPie/data
geneListPie/data/goslim.mouse.all.RData
geneListPie/data/kegg2.5.generic.RData
geneListPie/data/goslim.rat.BP.RData
geneListPie/data/goslim.yeast.BP.RData
geneListPie/data/goslim.rat.all.RData
geneListPie/data/goslim.mouse.MF.RData
geneListPie/data/goslim.human.BP.RData
geneListPie/data/goslim.mouse.CC.RData
geneListPie/data/goslim.human.CC.RData
geneListPie/data/goslim.yeast.all.RData
geneListPie/data/goslim.yeast.CC.RData
geneListPie/data/goslim.human.all.RData
geneListPie/data/goslim.human.MF.RData
geneListPie/data/goslim.mouse.BP.RData
geneListPie/data/datalist
geneListPie/data/goslim.rat.MF.RData
geneListPie/data/goslim.rat.CC.RData
geneListPie/data/goslim.yeast.MF.RData