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WorkflowSourcesTestsDescription
aCGH Survival Analysis

aCGH/aCGHBuildSurvivalData.R

aCGH/acgh-plot-survival.R

 

Plot survival curves for so-called copy number data

v16 User Guide page 46

Rancho Training Manual page 18

Box Plot with ANOVA

ANOVA/BuildANOVAData.R

ANOVA/BoxPlotLoader.R

RC2_test_analysis_Box_Plot_with_ANOVA

RC2_test_serial_low_dim

RC2_test_Metabolomics

RC2_test_miRNAseq

RC2_test_qPCR_miRNA

RC2_test_RBM

RC2_test_RNAseq

Box plot with ANOVA Analysis of Variance

v1.1 User Guide page 59

v16 User Guide page 48 

Rancho Training Manual page 13

Correlation Analysis

Correlation/BuildCorrelationData.R

Correlation/CorrelationLoader.r

RC2_test_serial_low_dim

 

v16 User Guide page 50 

Rancho Training Manual page 13

Forest Plot

(hidden in Advanced Workflows menu)

ForestPlot/BuildForestPlotData.R

ForestPlot/ForestPlotLoader.R

ForestPlot/forest-plot.R

ForestPlot/makeForestPlotForRCTs.R

 

 

v16 User Guide page 51

Frequency Plot for aCGH

aCGH/aCGHBuildFrequencyPlotData.R

aCGH/acgh-frequency-plot.R

 

 

v16 User Guide page 55 

Rancho Training Manual page 18

Group Test for aCGH

aCGH/aCGHBuildGroupTestData.R

aCGH/acgh-group-test.R

 

 

v16 User Guide page 56 

Rancho Training Manual page 18

Group Test for RNAseq

RNASeq/RNASeq-edgeR-DEanalysis.R

RNASeq/RNASeqGroupTestJobMapTemplate.txt

 

Group test for RNAseq-based read count observations

v16 User Guide page 57 

Rancho Training Manual page 18

Heatmap

Heatmap/BuildHeatmapData.R

Heatmap/HeatmapLoader.R

 

 

v1.1 User Guide page 49

v16 User Guide page 60 

Rancho Training Manual page 19

Hierarchical Clustering

Heatmap/BuildHeatmapData.R

Heatmap/HClusteredHeatmapLoader.R

 

 

v1.1 User Guide page 51

v16 User Guide page 61 

Rancho Training Manual page 19

IC50

IC50/BuildIC50Data.R

IC50/IC50Loader.R

 

IC50 Dose Response Curve

v16 User Guide page 66 
K-Means Clustering

Heatmap/BuildHeatmapData.R

Heatmap/KMeansHeatmap.R

 

 

v1.1 User Guide page 54

v16 User Guide page 63 

Rancho Training Manual page 19

Line Graph

LineGraph/BuildLinearData.R

LineGraph/LineGraphLoader.r

 

 

v16 User Guide page 68 

Rancho Training Manual page 14

Logistic Regression

LogisticRegression/BuildLogisticRegressionData.R

LogisticRegression/LogisticRegressionLoader.R

 

 

v16 User Guide page 69 

Rancho Training Manual page 14

Marker Selection

MarkerSelection/BuildMSData.R

MarkerSelection/MarkerSelection.R

 

 

v1.1 User Guide page 56

v16 User Guide page 64 

Rancho Training Manual page 19

PCA

PCA/BuildPCAData.R

PCA/LoadPCA.R

 

 

v1.1 User Guide page 61

v16 User Guide page 71 

Rancho Training Manual page 19

Scatter Plot with Linear Regression

ScatterPlot/BuildScatterData.R

ScatterPlot/ScatterPlotLoader.R

 

 

v1.1 User Guide page 64

v16 User Guide page 73 

Rancho Training Manual page 16

Survival Analysis

Survival/BuildSurvivalData.R

Survival/SurvivalCurveLoader.r

Survival/CoxRegressionLoader.r

 

 

v1.1 User Guide page 66

v16 User Guide page 77 

Rancho Training Manual page 17

Table with Fisher Test

TableWithFisher/BuildFisherData.R

TableWithFisher/FisherTableLoader.R

 

 

v1.1 User Guide page 69

v16 User Guide page 78 

Rancho Training Manual page 17

Waterfall

Waterfall/BuildWaterfallData.R

Waterfall/WaterfallPlotLoader.R

 

 

v16 User Guide page 81 
GWAS PlinkGWAS plink plugin (no R code) 

 

New in release 16.2
GWAS Analysis (GWAS tab)Manhattan/Manhattan.R 

 

v16 User Guide page 126 

Rancho Training Manual page 33

GWAS QQ Plot (GWAS tab)QQ/QQPlot.R 

 

v16 User Guide page 123 

Rancho Training Manual page 33