Files in gevaertlab/AMARETTO
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
.Rbuildignore
.gitignore
AMARETTO_EXAMPLE/AMARETTO.R
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/amaretto_download.R
R/amaretto_functions.R
R/amaretto_htmlreport.R
R/amaretto_initialize.R
R/amaretto_preprocess.R
R/amaretto_run.R
R/amaretto_vizualize.R
R/data.R
README.md
data/BatchData.rda
data/Driver_Genes.rdata
data/MsigdbMapping.rda
data/ProcessedDataLIHC.rda
inst/extdata/MethylStates.rda
inst/extdata/Module1_LIHC.png
inst/extdata/logo.jpg
inst/templates/H.C2CP.genesets.gmt
inst/templates/TemplateIndexPage.Rmd
inst/templates/TemplateReportModule.Rmd
man/AMARETTO_CreateModuleData.Rd
man/AMARETTO_CreateRegulatorPrograms.Rd
man/AMARETTO_Download.Rd
man/AMARETTO_EvaluateTestSet.Rd
man/AMARETTO_ExportResults.Rd
man/AMARETTO_HTMLreport.Rd
man/AMARETTO_Initialize.Rd
man/AMARETTO_LarsenBased.Rd
man/AMARETTO_LearnRegulatoryProgramsLarsen.Rd
man/AMARETTO_Preprocess.Rd
man/AMARETTO_ReassignGenesToClusters.Rd
man/AMARETTO_Run.Rd
man/AMARETTO_VisualizeModule.Rd
man/BatchData.Rd
man/Beta.NA.Rd
man/ComBat_NoFiles.Rd
man/CreateRegulatorData.Rd
man/Driver_Genes.Rd
man/FindTranscriptionallyPredictive_CNV.Rd
man/GeneSetDescription.Rd
man/GmtFromModules.Rd
man/HyperGTestGeneEnrichment.Rd
man/L.Rd
man/Lambda_Sequence.Rd
man/MsigdbMapping.Rd
man/Preprocess_MAdata.Rd
man/ProcessedDataLIHC.Rd
man/Save_CancerSite.Rd
man/TCGA_BatchCorrection_MolecularData.Rd
man/TCGA_GENERIC_BatchCorrection.Rd
man/TCGA_GENERIC_CheckBatchEffect.Rd
man/TCGA_GENERIC_CleanUpSampleNames.Rd
man/TCGA_GENERIC_GetSampleGroups.Rd
man/TCGA_GENERIC_MergeData.Rd
man/TCGA_Load_GISTICdata.Rd
man/TCGA_Load_MolecularData.Rd
man/aprior.Rd
man/bprior.Rd
man/build.design.Rd
man/cacheResource.Rd
man/computeGisticURL.Rd
man/design.mat.Rd
man/filter.absent.Rd
man/geneFiltering.Rd
man/get_firehoseData.Rd
man/int.eprior.Rd
man/it.sol.Rd
man/list.batch.Rd
man/plot_run_history.Rd
man/postmean.Rd
man/postvar.Rd
man/printf.Rd
man/readGMT.Rd
man/read_gct.Rd
man/trim.dat.Rd
man/write_gct.Rd
tests/testthat.R
tests/testthat/test_AMARETTO.R
vignettes/_output.yaml
vignettes/_site.yml
vignettes/amaretto.Rmd
vignettes/include/after_body.html
vignettes/include/before_body.html
vignettes/include/header.html
vignettes/include/site.css
