Man pages for bic-mskcc/halo
Analyze and visualize Halo data

addMissingMarkersAdd missing markers
cleanDataClean data table
cleanMarkersClean marker file
countMarkersGenerate a XLSX file of counts for all markers in a given...
get_custom_colorsGet marker colors
get_marker_colorsGet marker colors
getSheetOrderGet order of workbook sheets for final excel file
g_legendExtract a legend from a gplot
loadHaloLoad data from *.rda file
logMsgLog message to file and screen if specified
logParamsLog project parameters
markerStatsFileGenerate name of output file for marker stats based on input...
medianRowCreate median row
plot_marker_percentagesMake a grid of pie charts, one for each given marker showing...
projectFileNameGenerate name of output file for marker stats based on input...
projectParamsBuild list of project parameters and values by reading...
remove_exclusionsRemove from counts tibble any FOV to be excluded
removeExtraMarkersRemove from data markers that are not in marker file
remove_legendRemove a legend from a gplot
split_by_fovSplit data in *.rda file by FOV (SPOT)
trimImageRemove cells near edge of FOV from dataset
validateMarkersModify data to sync to markers in marker file
validateSingleFOVFileMake sure list of unique FOVs contains only one element
writeXLSXsheetShortcut to write a XLSX file
bic-mskcc/halo documentation built on Jan. 27, 2018, 12:19 a.m.