TABLE 1.

List of tasks, steps, methods, and parameters of GeenaR web user’s interface.

Task	Step	Method	Parameters
Reading	Import files
	Read target file
	Acquire metadata
Quality control	Create log file
	Detection of outliers
	Plot raw spectra
Trimming	Trim raw spectra		Min-Max, User
	Plot trimmed spectra
Cleaning	Variance stabilization	sqrt, logE, log2, log10
	Plot stabilized spectra
	Smoothing	Savitzky-Golay, Moving Average	Half window size
	Plot smoothed spectra
	Baseline correction	SNIP	Number of iterations
		Top Hat	Half window size
		Convex hull, median
	Plot corrected spectra
	Normalization	TIC, PQN, median
	Plot normalized spectra
Averaging and aligning	Average replicates	Mean, median, sum
	Plot averaged spectra
	Align samples	a. MAD, Super Smoother	Half window size, SNR
		b. Lowess, linear, quadratic, cubic (*)	Tolerance
	Plot aligned spectra
Peak extraction	Peak detection	MAD, Super Smoother	Half window size, SNR
	Peak binning	Strict, relaxed	Tolerance
	Peak filtering		Minimum frequency
	Create feature matrix
	Create heatmap
	Plot peaks
Clustering and visualization	PCA
	Plot PCs and top loadings
	Estimate number of clusters	Gap statistic, silhouette	User
	Clustering	Ward, complete, average, median
	Plot clusters estimation
	Plot dendrogram
Reporting	Generate html report with spectra
	Generate html report with R code

The tasks are in the first column, the steps are in the second column, the methods are in the third column, and the parameters are in the fourth column. Rows indicate methods and parameters related to the corresponding steps. Selectable steps-methods are slightly different from the web page. (*) Two different kinds of methods for the same step.