Files in seshadrilab/COMPASSHelpers
Collection of helper functions for analyzing FCM data
DESCRIPTION
ExampleRunThrough/1_QC_Example.R
ExampleRunThrough/2_SetupGatingSetList_Example.R
ExampleRunThrough/3_RunCompass_Example.R
ExampleRunThrough/4_PostCompassPlots_Example.R
ExampleRunThrough/output/CompassOutput/CD4/4+_Ag85A/FS_4+_Ag85A.txt
ExampleRunThrough/output/CompassOutput/CD4/4+_Ag85A/HeatmapLogPostResponse_4+Ag85A.png
ExampleRunThrough/output/CompassOutput/CD4/4+_Ag85A/HeatmapMeanProbResponse_4+Ag85A.png
ExampleRunThrough/output/CompassOutput/CD4/4+_Ag85A/PFS_4+_Ag85A.txt
ExampleRunThrough/output/CompassOutput/CD4/4+_Ag85B/FS_4+_Ag85B.txt
ExampleRunThrough/output/CompassOutput/CD4/4+_Ag85B/HeatmapLogPostResponse_4+Ag85B.png
ExampleRunThrough/output/CompassOutput/CD4/4+_Ag85B/HeatmapMeanProbResponse_4+Ag85B.png
ExampleRunThrough/output/CompassOutput/CD4/4+_Ag85B/PFS_4+_Ag85B.txt
ExampleRunThrough/output/CompassOutput/CD4/4+_CFP-10/FS_4+_CFP-10.txt
ExampleRunThrough/output/CompassOutput/CD4/4+_CFP-10/HeatmapLogPostResponse_4+CFP-10.png
ExampleRunThrough/output/CompassOutput/CD4/4+_CFP-10/HeatmapMeanProbResponse_4+CFP-10.png
ExampleRunThrough/output/CompassOutput/CD4/4+_CFP-10/PFS_4+_CFP-10.txt
ExampleRunThrough/output/CompassOutput/CD4/4+_CMV/FS_4+_CMV.txt
ExampleRunThrough/output/CompassOutput/CD4/4+_CMV/HeatmapLogPostResponse_4+CMV.png
ExampleRunThrough/output/CompassOutput/CD4/4+_CMV/HeatmapMeanProbResponse_4+CMV.png
ExampleRunThrough/output/CompassOutput/CD4/4+_CMV/PFS_4+_CMV.txt
ExampleRunThrough/output/CompassOutput/CD4/4+_ESAT-6/FS_4+_ESAT-6.txt
ExampleRunThrough/output/CompassOutput/CD4/4+_ESAT-6/HeatmapLogPostResponse_4+ESAT-6.png
ExampleRunThrough/output/CompassOutput/CD4/4+_ESAT-6/HeatmapMeanProbResponse_4+ESAT-6.png
ExampleRunThrough/output/CompassOutput/CD4/4+_ESAT-6/PFS_4+_ESAT-6.txt
ExampleRunThrough/output/CompassOutput/CD4/4+_PHA/FS_4+_PHA.txt
ExampleRunThrough/output/CompassOutput/CD4/4+_PHA/HeatmapLogPostResponse_4+PHA.png
ExampleRunThrough/output/CompassOutput/CD4/4+_PHA/HeatmapMeanProbResponse_4+PHA.png
ExampleRunThrough/output/CompassOutput/CD4/4+_PHA/PFS_4+_PHA.txt
ExampleRunThrough/output/CompassOutput/CD4/4+_TB10.4/FS_4+_TB10.4.txt
ExampleRunThrough/output/CompassOutput/CD4/4+_TB10.4/HeatmapLogPostResponse_4+TB10.4.png
ExampleRunThrough/output/CompassOutput/CD4/4+_TB10.4/HeatmapMeanProbResponse_4+TB10.4.png
ExampleRunThrough/output/CompassOutput/CD4/4+_TB10.4/PFS_4+_TB10.4.txt
ExampleRunThrough/output/CompassOutput/CD4/CD4HeatmapsMeanProbResponse.pdf
ExampleRunThrough/output/CompassOutput/CD4/combinepngsCD4.sh
ExampleRunThrough/output/CompassOutput/CD8/8+_Ag85A/FS_8+_Ag85A.txt
ExampleRunThrough/output/CompassOutput/CD8/8+_Ag85A/HeatmapLogPostResponse_8+Ag85A.png
ExampleRunThrough/output/CompassOutput/CD8/8+_Ag85A/PFS_8+_Ag85A.txt
ExampleRunThrough/output/CompassOutput/CD8/8+_Ag85B/FS_8+_Ag85B.txt
ExampleRunThrough/output/CompassOutput/CD8/8+_Ag85B/HeatmapLogPostResponse_8+Ag85B.png
ExampleRunThrough/output/CompassOutput/CD8/8+_Ag85B/PFS_8+_Ag85B.txt
ExampleRunThrough/output/CompassOutput/CD8/8+_CFP-10/FS_8+_CFP-10.txt
ExampleRunThrough/output/CompassOutput/CD8/8+_CFP-10/HeatmapLogPostResponse_8+CFP-10.png
ExampleRunThrough/output/CompassOutput/CD8/8+_CFP-10/PFS_8+_CFP-10.txt
ExampleRunThrough/output/CompassOutput/CD8/8+_CMV/FS_8+_CMV.txt
ExampleRunThrough/output/CompassOutput/CD8/8+_CMV/HeatmapLogPostResponse_8+CMV.png
ExampleRunThrough/output/CompassOutput/CD8/8+_CMV/PFS_8+_CMV.txt
ExampleRunThrough/output/CompassOutput/CD8/8+_ESAT-6/FS_8+_ESAT-6.txt
ExampleRunThrough/output/CompassOutput/CD8/8+_ESAT-6/HeatmapLogPostResponse_8+ESAT-6.png
ExampleRunThrough/output/CompassOutput/CD8/8+_ESAT-6/PFS_8+_ESAT-6.txt
ExampleRunThrough/output/CompassOutput/CD8/8+_PHA/FS_8+_PHA.txt
ExampleRunThrough/output/CompassOutput/CD8/8+_PHA/HeatmapLogPostResponse_8+PHA.png
ExampleRunThrough/output/CompassOutput/CD8/8+_PHA/HeatmapMeanProbResponse_8+PHA.png
ExampleRunThrough/output/CompassOutput/CD8/8+_PHA/PFS_8+_PHA.txt
ExampleRunThrough/output/CompassOutput/CD8/8+_TB10.4/FS_8+_TB10.4.txt
ExampleRunThrough/output/CompassOutput/CD8/8+_TB10.4/HeatmapLogPostResponse_8+TB10.4.png
ExampleRunThrough/output/CompassOutput/CD8/8+_TB10.4/PFS_8+_TB10.4.txt
ExampleRunThrough/output/PostCompassPlots/Boxplot_4+_ESAT-6_IFNg+154+IL2+TNFa+.png
ExampleRunThrough/output/PostCompassPlots/Boxplot_4+_TB10.4_IFNg+154+IL2+TNFa+.png
ExampleRunThrough/output/PostCompassPlots/FACSplot_PATIENT ID_03-0311_4+_ESAT-6_IFNg+154+IL2+TNFa+.png
ExampleRunThrough/output/PostCompassPlots/FACSplot_PATIENT ID_03-0311_4+_TB10.4_IFNg+154+IL2+TNFa+.png
ExampleRunThrough/output/PostCompassPlots/StackedHeatmapMeanProbResponse_CD4.png
ExampleRunThrough/output/QCResults/QC_Annotated_Counts__S_14-_LV_L_3+_Batch1GatingSet.txt
ExampleRunThrough/output/QCResults/QC_Annotated_Counts__S_14-_LV_L_3+_Batch2GatingSet.txt
ExampleRunThrough/output/QCResults/QC_Annotated_Counts__S_14-_LV_L_3+_Batch3GatingSet.txt
ExampleRunThrough/output/QCResults/QC_Annotated_Counts__S_14-_LV_L_3+_Batch4GatingSet.txt
ExampleRunThrough/output/QCResults/QC_Annotated_Counts__S_14-_LV_L_3+_Batch5GatingSet.txt
ExampleRunThrough/output/QCResults/QC_Boxplot__S_14-_LV_L_3+_Counts_By_PATIENT ID_Batch1GatingSet.png
ExampleRunThrough/output/QCResults/QC_Boxplot__S_14-_LV_L_3+_Counts_By_PATIENT ID_Batch2GatingSet.png
ExampleRunThrough/output/QCResults/QC_Boxplot__S_14-_LV_L_3+_Counts_By_PATIENT ID_Batch3GatingSet.png
ExampleRunThrough/output/QCResults/QC_Boxplot__S_14-_LV_L_3+_Counts_By_PATIENT ID_Batch4GatingSet.png
ExampleRunThrough/output/QCResults/QC_Boxplot__S_14-_LV_L_3+_Counts_By_PATIENT ID_Batch5GatingSet.png
NAMESPACE
R/AddBooleanGate.R
R/BoxplotBooleanSubsetcellProportions.R
R/BoxplotSubsetProportionStats.R
R/CellCountsQC.R
R/CompassStratifiedBackgroundCorrectedProportionsBoxplots.R
R/CompassSubsetComparisons.R
R/CytokineSpecificSubsetComparison.R
R/FunctionalityScoreLinePlot.R
R/FunctionalityScorePlot.R
R/GenericCompassWrapper.R
R/HighlightBooleanSubsetFlowPlot.R
R/LinePlotBooleanSubsetcellProportions.R
R/OrderHeatmapColumnsForCytokine.R
R/PrepareGatingSetList4Compass.R
R/runTSNE.R
README.md
man/addBooleanGate.Rd
man/boxplot.boolean.subset.proportions.Rd
man/boxplot.cell.counts.Rd
man/boxplot.subset.proportion.stats.Rd
man/boxplotsCompassSubsetBgCorrPropStratified.Rd
man/compass.subset.comparisons.Rd
man/cytokine.specific.subset.comparison.Rd
man/fs.line.plot.Rd
man/fs.plot.Rd
man/generic.compass.wrapper.Rd
man/getCatsAndSubsetNames.Rd
man/highlight.boolean.subset.flow.plot.Rd
man/lineplot.boolean.subset.proportions.Rd
man/orderHeatmapColumnsByCytokinePresence.Rd
man/prepare.gating.set.list.4.compass.Rd
man/run.compass.once.Rd
man/runOneSense.Rd
man/runTSNE.Rd
man/sampleGatingSetForTsne.Rd
