FunCluster: Functional Profiling of Microarray Expression Data

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FunCluster performs a functional analysis of microarray expression data based on Gene Ontology & KEGG functional annotations. From expression data and functional annotations FunCluster builds classes of putatively co-regulated biological processes through a specially designed clustering procedure.

Author
Corneliu Henegar <corneliu@henegar.info>
Date of publication
2012-07-23 10:35:30
Maintainer
Corneliu Henegar <corneliu@henegar.info>
License
GPL (>= 2)
Version
1.09
URLs

View on CRAN

Man pages

adipose
Gene Expression in Human White Adipose Tissue
annotate
Internal routine or variable
AnnotationIndirecte
Internal routine or variable
Annotations
Functional Profiling of Microarray RNA Expression Data
annot.date
Internal routine or variable
annot.list
Internal routine or variable
ChargerKegg
Internal routine or variable
cluster.c
Internal routine or variable
clusterm.cc
Internal routine or variable
clusterm.cs
Internal routine or variable
down
Internal routine or variable
fdr
Internal routine or variable
fdr.adjust
Internal routine or variable
fdr.basic
Internal routine or variable
fdr.master
Internal routine or variable
filter.genes
Internal routine or variable
FunCluster
Functional Profiling of Microarray Expression Data
FunCluster.R-package
Functional Profiling of Microarray Expression Data
f.version
Internal routine or variable
gene.correl
Internal routine or variable
GeneInfo
Internal routine or variable
GeneInfoSC
Internal routine or variable
genes.lst
Internal routine or variable
goAndLL
Internal routine or variable
GO.terms.hierarchy
Internal routine or variable
GO.terms.name
Internal routine or variable
HS.GO.DIR.BP.file.annot
Internal routine or variable
HS.GO.DIR.CC.file.annot
Internal routine or variable
HS.GO.DIR.MF.file.annot
Internal routine or variable
HS.GO.IND.BP.file.annot
Internal routine or variable
HS.GO.IND.CC.file.annot
Internal routine or variable
HS.GO.IND.MF.file.annot
Internal routine or variable
HS.KEGG.file.annot
Internal routine or variable
HS.locus.cyto
Internal routine or variable
HS.locus.name
Internal routine or variable
insulin
Insulin Coordinated Regulation of Gene Expression in Human...
Kegg
Internal routine or variable
KEGG.terms.name
Internal routine or variable
location.analysis
Internal routine or variable
main.loop
Internal routine or variable
MakeCorrespondanceLLGO
Internal routine or variable
MakeGoHierarchy
Internal routine or variable
MakeGoTerms
Internal routine or variable
MakeLocusNames
Internal routine or variable
MiseEnFormeKegg
Internal routine or variable
MiseEnFormeKeggSC
Internal routine or variable
MM.GO.DIR.BP.file.annot
Internal routine or variable
MM.GO.DIR.CC.file.annot
Internal routine or variable
MM.GO.DIR.MF.file.annot
Internal routine or variable
MM.GO.IND.BP.file.annot
Internal routine or variable
MM.GO.IND.CC.file.annot
Internal routine or variable
MM.GO.IND.MF.file.annot
Internal routine or variable
MM.KEGG.file.annot
Internal routine or variable
MM.locus.cyto
Internal routine or variable
MM.locus.name
Internal routine or variable
pclust
Internal routine or variable
preliminary
Internal routine or variable
prop.alt
Internal routine or variable
pterm
Internal routine or variable
pvalues
Internal routine or variable
ref.list
Internal routine or variable
resclust
Internal routine or variable
resterm
Internal routine or variable
SC.GO.DIR.BP.file.annot
Internal routine or variable
SC.GO.DIR.CC.file.annot
Internal routine or variable
SC.GO.DIR.MF.file.annot
Internal routine or variable
SC.GO.IND.BP.file.annot
Internal routine or variable
SC.GO.IND.CC.file.annot
Internal routine or variable
SC.GO.IND.MF.file.annot
Internal routine or variable
SC.KEGG.file.annot
Internal routine or variable
SC.locus.cyto
Internal routine or variable
SC.locus.name
Internal routine or variable
storey
Internal routine or variable
term.compare
Internal routine or variable
TroisiemeFiltrage
Internal routine or variable
up
Internal routine or variable

Files in this package

FunCluster
FunCluster/MD5
FunCluster/R
FunCluster/R/FunCluster.R
FunCluster/R/Annotations.R
FunCluster/R/sysdata.rda
FunCluster/copying
FunCluster/man
FunCluster/man/SC.GO.DIR.BP.file.annot.Rd
FunCluster/man/HS.locus.name.Rd
FunCluster/man/storey.Rd
FunCluster/man/annotate.Rd
FunCluster/man/MM.GO.IND.BP.file.annot.Rd
FunCluster/man/FunCluster.R-package.Rd
FunCluster/man/MakeGoTerms.Rd
FunCluster/man/MM.GO.DIR.BP.file.annot.Rd
FunCluster/man/gene.correl.Rd
FunCluster/man/HS.GO.DIR.BP.file.annot.Rd
FunCluster/man/pterm.Rd
FunCluster/man/HS.GO.IND.BP.file.annot.Rd
FunCluster/man/pclust.Rd
FunCluster/man/SC.locus.name.Rd
FunCluster/man/AnnotationIndirecte.Rd
FunCluster/man/MakeGoHierarchy.Rd
FunCluster/man/adipose.Rd
FunCluster/man/SC.KEGG.file.annot.Rd
FunCluster/man/KEGG.terms.name.Rd
FunCluster/man/Annotations.Rd
FunCluster/man/MM.GO.DIR.CC.file.annot.Rd
FunCluster/man/GO.terms.name.Rd
FunCluster/man/HS.KEGG.file.annot.Rd
FunCluster/man/MiseEnFormeKeggSC.Rd
FunCluster/man/MakeCorrespondanceLLGO.Rd
FunCluster/man/SC.GO.IND.MF.file.annot.Rd
FunCluster/man/main.loop.Rd
FunCluster/man/prop.alt.Rd
FunCluster/man/annot.date.Rd
FunCluster/man/resclust.Rd
FunCluster/man/HS.locus.cyto.Rd
FunCluster/man/MM.GO.DIR.MF.file.annot.Rd
FunCluster/man/fdr.master.Rd
FunCluster/man/Kegg.Rd
FunCluster/man/TroisiemeFiltrage.Rd
FunCluster/man/MM.locus.cyto.Rd
FunCluster/man/pvalues.Rd
FunCluster/man/annot.list.Rd
FunCluster/man/term.compare.Rd
FunCluster/man/up.Rd
FunCluster/man/SC.GO.IND.BP.file.annot.Rd
FunCluster/man/MakeLocusNames.Rd
FunCluster/man/FunCluster.Rd
FunCluster/man/HS.GO.IND.MF.file.annot.Rd
FunCluster/man/MiseEnFormeKegg.Rd
FunCluster/man/GeneInfoSC.Rd
FunCluster/man/MM.GO.IND.MF.file.annot.Rd
FunCluster/man/fdr.basic.Rd
FunCluster/man/fdr.adjust.Rd
FunCluster/man/HS.GO.IND.CC.file.annot.Rd
FunCluster/man/MM.KEGG.file.annot.Rd
FunCluster/man/ChargerKegg.Rd
FunCluster/man/filter.genes.Rd
FunCluster/man/goAndLL.Rd
FunCluster/man/SC.locus.cyto.Rd
FunCluster/man/ref.list.Rd
FunCluster/man/HS.GO.DIR.CC.file.annot.Rd
FunCluster/man/clusterm.cs.Rd
FunCluster/man/GO.terms.hierarchy.Rd
FunCluster/man/preliminary.Rd
FunCluster/man/MM.locus.name.Rd
FunCluster/man/resterm.Rd
FunCluster/man/clusterm.cc.Rd
FunCluster/man/MM.GO.IND.CC.file.annot.Rd
FunCluster/man/SC.GO.DIR.MF.file.annot.Rd
FunCluster/man/SC.GO.DIR.CC.file.annot.Rd
FunCluster/man/fdr.Rd
FunCluster/man/insulin.Rd
FunCluster/man/f.version.Rd
FunCluster/man/genes.lst.Rd
FunCluster/man/down.Rd
FunCluster/man/location.analysis.Rd
FunCluster/man/cluster.c.Rd
FunCluster/man/HS.GO.DIR.MF.file.annot.Rd
FunCluster/man/SC.GO.IND.CC.file.annot.Rd
FunCluster/man/GeneInfo.Rd
FunCluster/NAMESPACE
FunCluster/DESCRIPTION
FunCluster/data
FunCluster/data/adipose.rda
FunCluster/data/insulin.rda