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 |