GEoDE introdction

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.

packages site

https://cran.r-project.org/web/packages/GeoDE/index.html#:~:text=GeoDE%3A%20A%20geometrical%20Approach%20to%20Differential%20expression%20and,differential%20expression%20and%20can%20also%20perform%20gene-set%20enrichment.

Reference manual

https://cran.r-project.org/web/packages/GeoDE/GeoDE.pdf

Installation

install.packages("GeoDE")
#| Depends: R>2.10, Matrix, MASS
library(GeoDE)

Given gene expression data from two classes
logical replicates in each class, this package can be used to extract the most significant genes and gene-sets.
Differential expression is characterised with a single direction in expression space, which can be interpreted to extract the most signiicant genes: this is achieved with the chdirAnalysis function.
Once the characeristic direction has been calculated gene-set enrichmnet can be evaluated using the PAEAAnalysis function. The user is free to use any library of gene-sets, however, included in this package is a broad range of gene-set libraries listed below:
BioCarta_pathways.gmt
Cancer_Cell_Line_Encyclopedia.gmt
ChEA.gmt
Chromosome_location.gmt
CORUM.gmt.gmt
GeneOntology_BP.gmt
GeneOntology_CC.gmt
GeneOntology_MF.gmt
GeneSigDB.gmt
Genome_Browser_PWMs.gmt
HMDB_Metabolites.gmt
Human_Gene_Atlas.gmt
KEA.gmt
KEGG_pathways.gmt
MGI_MP_top3.gmt
MGI_MP_top4.gmt
microRNA.gmt
Mouse_Gene_Atlas.gmt
NCI60.gmt
NURSA-IPMS.gmt
OMIM_disease_genes.gmt
OMIM_Expanded.gmt
Pfam-InterPro-domains.gmt
PPI_Hub_Proteins.gmt
Reactome_pathways.gmt
TF_PPIs.gmt
VirusMINT.gmt
WikiPathways_pathways.gmt