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

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

Author
Neil R. Clark and Avi Ma'ayan
Date of publication
2014-07-31 07:17:53
Maintainer
Neil Clark <neil.clark@mssm.edu>
License
GPL-2
Version
1.0

View on CRAN

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.

Files in this package

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