GeoDE: A geometrical Approach to Differential expression and gene-set enrichment
Version 1.0

Given expression data this package calculate a multivariate geometrical characterization of the differential expression and can also perform gene-set enrichment.

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AuthorNeil R. Clark and Avi Ma'ayan
Date of publication2014-07-31 07:17:53
MaintainerNeil Clark <neil.clark@mssm.edu>
LicenseGPL-2
Version1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("GeoDE")

Man pages

AllGMTfiles: The gmt files included in GeoDE
chdirAnalysis: A Function to Perform Characteristic Direction Analysis.
example_expression_data: Example Expression Data
example_gammas: Example Gamma Value
example_sampleclass: Example Sample Class Factor
GeoDE-package: Differential Expression and Enrichment Analysis with...
gmt: The currently loaded gmtfile
multigmtPAEAAnalysis: A Function to Evaluate Gene-Set Enrichment Using PAEA Over...
PAEAAnalysis: A Function to Evaluate Gene-Set Enrichment Using PAEA.

Functions

AllGMTfiles Man page
GeoDE Man page
GeoDE-package Man page
PAEA Source code
PAEAAnalysis Man page Source code
chdirAnalysis Man page Source code
chdirSig Source code
chdirplots Source code
example_expression_data Man page
example_gammas Man page
example_sampleclass Man page
gmt Man page
multigmtPAEAAnalysis Man page Source code

Files

NAMESPACE
data
data/microRNA.gmt.RData
data/Chromosome_location.gmt.RData
data/KEGG_pathways.gmt.RData
data/Cancer_Cell_Line_Encyclopedia.gmt.RData
data/GeneOntology_MF.gmt.RData
data/example_expression_data.RData
data/HMDB_Metabolites.gmt.RData
data/OMIM_disease_genes.gmt.RData
data/NCI60.gmt.RData
data/MGI_MP_top3.gmt.RData
data/OMIM_Expanded.gmt.RData
data/AllGMTfiles.RData
data/Reactome_pathways.gmt.RData
data/PPI_Hub_Proteins.gmt.RData
data/ChEA.gmt.RData
data/GeneOntology_CC.gmt.RData
data/Genome_Browser_PWMs.gmt.RData
data/Pfam-InterPro-domains.gmt.RData
data/NURSA-IPMS.gmt.RData
data/KEA.gmt.RData
data/WikiPathways_pathways.gmt.RData
data/Human_Gene_Atlas.gmt.RData
data/BioCarta_pathways.gmt.RData
data/VirusMINT.gmt.RData
data/CORUM.gmt.RData
data/datalist
data/GeneSigDB.gmt.RData
data/GeneOntology_BP.gmt.RData
data/example_gammas.RData
data/TF_PPIs.gmt.RData
data/MGI_MP_top4.gmt.RData
data/Mouse_Gene_Atlas.gmt.RData
data/example_sampleclass.RData
R
R/ChDir-06.R
MD5
DESCRIPTION
man
man/AllGMTfiles.Rd
man/example_gammas.Rd
man/GeoDE-package.Rd
man/example_sampleclass.Rd
man/gmt.Rd
man/example_expression_data.Rd
man/PAEAAnalysis.Rd
man/chdirAnalysis.Rd
man/multigmtPAEAAnalysis.Rd
GeoDE documentation built on May 19, 2017, 9:30 a.m.