Files in waldronlab/MultiAssayExperiment.TCGA
Pipeline for the integration of multi-omics experiments in Bioconductor
.Rbuildignore
.Renviron
.gitignore
DESCRIPTION
MAEOinfo.csv
NAMESPACE
R/buildMultiAssayExperiment.R
R/data.R
R/dataDirectories.R
R/getDataLinks.R
R/getDiseaseCodes.R
R/loadData.R
R/pipelineTools.R
R/saveMapData.R
R/saveNupload.R
R/saveRTCGAdata.R
R/updateInfo.R
R/uploadAzure.R
R/utils.R
README.md
data-raw/ExcelPreprocess/OV_preproc.R
data-raw/ExcelPreprocess/SKCM_preproc.R
data-raw/ExcelPreprocess/excel_BLCA_preproc.R
data-raw/ExcelPreprocess/excel_KICH_preproc.R
data-raw/ExcelPreprocess/excel_KIRP_preproc.R
data-raw/ExcelPreprocess/excel_LAML_preproc.R
data-raw/ExcelPreprocess/excel_LGGGBM_preproc.R
data-raw/ExcelPreprocess/excel_LUAD_preproc.R
data-raw/ExcelPreprocess/excel_LUSC_preproc.R
data-raw/ExcelPreprocess/excel_SKCM_preproc.R
data-raw/ExcelPreprocess/excel_position.R
data-raw/ToolboxClinNames.R
data-raw/brcaMerge.R
data-raw/checkClinicalCuration.R
data-raw/checkMeta.R
data-raw/checkSubtypeCuration.R
data-raw/cleanDuplicates.R
data-raw/codesCurated.R
data-raw/createSubtypeMaps.R
data-raw/mergeClinicalCuration.R
data-raw/merge_curated_LW.R
data-raw/modify_se_links.R
data-raw/rename_methyl_s3.R
data-raw/rm_noRunDate.R
data-raw/rm_old_methyl.R
data-raw/subtypeMaps.R
data-raw/subtypes_curation.txt
data-raw/writeSubtypeCuration.R
data/curationAvailable.rda
exec/getRawData.sh
exec/pullRDS.sh
exec/runPipeline.R
exec/runPipeline.sh
exec/start.sh
exec/updateObj.sh
inst/extdata/clinicalColnames.rds
inst/scripts/checkMultipleMerges.R
inst/scripts/downloadDropbox.R
inst/scripts/getRawData.R
inst/scripts/metadataUpdate.R
inst/scripts/renameRDS.R
inst/scripts/updateRTCGA.R
man/buildMultiAssayExperiment.Rd
man/curationAvailable.Rd
man/dataDirectories.Rd
man/getDiseaseCodes.Rd
man/loadData.Rd
man/saveNupload.Rd
man/saveRTCGAdata.Rd
man/updateInfo.Rd
man/uploadAzure.Rd
vignettes/MultiAssayPipeline.Rmd
