Identify oncogenes and tumor suppressor genes from omics data


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Documentation for package ‘Moonlight2R’ version 1.0.0

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confidence confidence
cscape_somatic_output Cscape-somatic annotations of TCGA-LUAD
dataDMA Output example from the function Driver Mutation Analysis
dataFEA Functional enrichment analysis
dataFilt Gene expression data from TCGA-LUAD
dataGLS Literature search of driver genes
dataGRN Gene regulatory network
dataGRN_no_noise Gene regulatory network
dataMAF Mutation data from TCGA LUAD
dataPRA Output example from function Pattern Recognition Analysis
dataURA Upstream regulator analysis
dataURA_plot Upstream regulator analysis
DEGsmatrix Differentially expressed genes
DEG_Mutations_Annotations Differentially expressed genes's Mutations
DiseaseList Cancer-related biological processes
DMA DMA
EAGenes Information about genes
EncodePromoters Promoters
FEA FEA
GEO_TCGAtab Information on GEO and TCGA data
getDataGEO getDataGEO
GLS GLS This function carries out gene literature search.
GRN Generate network
GSEA GSEA
knownDriverGenes Information of known cancer driver genes from COSMIC
LiftMAF LiftMAF
listMoonlight List of oncogenic mediators of 5 TCGA cancer types
LOC_protein Level of Consequence: Protein
LOC_transcription Level of Consequence: Transcription
LOC_translation Level of Consequence: Translation
LPA LPA
MAFtoCscape MAFtoCscape
moonlight moonlight pipeline
NCG Network of Cancer Genes 7.0
Oncogenic_mediators_mutation_summary Oncogenic Mediators Mutation Summary
plotCircos plotCircos
plotDMA plotDMA
plotFEA plotFEA
plotHeatmap plotHeatmap
plotMoonlight plotMoonlight
plotNetworkHive plotNetworkHive: Hive network plot
plotURA plotURA: Upstream regulatory analysis heatmap plot
PRA Pattern Recognition Analysis (PRA)
PRAtoTibble PRAtoTibble
RunCscape_somatic RunCscape_somatic
tabGrowBlock Information of growing/blocking characteristics of 101 biological processes
URA URA Upstream Regulator Analysis