# Identify oncogenes and tumor suppressor genes from omics data

## Documentation for package ‘MoonlightR’ version 1.38.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

dataFilt | Gene Expression (Rnaseqv2) data from TCGA LUAD
dataGRN | GRN gene regulatory network output
dataURA | Output example from function Upstram Regulator Analysis
DEGsmatrix | DEG Differentially expressed genes
DiseaseList | Information on 101 biological processes
DPA | DPA
EAGenes | Information about genes
FEA | FEA
GDCprojects | Information on GDC projects
geneInfo | Information about genes for normalization
GEO_TCGAtab | Information on GEO data (and overlap with TCGA)#' A data set containing the following data:
getDataGEO | getDataGEO
getDataTCGA | getDataTCGA
GRN | Generate network
GSEA | GSEA
knownDriverGenes | Information on known cancer driver gene from COSMIC
listMoonlight | Output list from Moonlight
LPA | LPA
moonlight | moonlight pipeline
MoonlightR | MoonlightR
plotCircos | plotCircos
plotFEA | plotFEA
plotNetworkHive | plotNetworkHive: Hive network plot
plotURA | plotURA: Upstream regulatory analysis heatmap plot
PRA | Pattern Recognition Analysis (PRA)
tabGrowBlock | Information growing/blocking characteristics for 101 selected biological processes
URA | URA Upstream Regulator Analysis