| E3Axes | Draw axes and labels on x/y, using Rcssplot |
| E3CalcAcrossGroupIntervalRescaleFactors | Estimate an interval rescale factor for each feature/gene... |
| E3CalcWithinGroupIntervalRescaleFactors | Estimates an interval rescale factor for each feature/gene... |
| E3CompareSignatures | Collect metrics (Jaccard, Overlap, Fisher) describing to what... |
| E3CompareVectors | take two vectors A, B returns a list with elements in A only,... |
| E3DEscore | Compute a score summarizing a fold-change and a z-value into... |
| E3dist.euclidean | Compute euclidean distances between all pairs of samples |
| E3dist.spearman | Compute spearman pseudo-distances between all pairs of... |
| E3DrawMarkerLegend | Draw a vertical legend with markers (circles, boxes, and... |
| E3DrawScaleLegend | Draw a vertical recrangle with a color scale and labels |
| E3GetDEScores | Compute DE scores for a single sample. |
| E3GetExpressedGenes | Determine genes that are expressed in a dataset. Expressed... |
| E3GetFisherP | Compute fisher p-value: selection of two vectors from a... |
| E3GetGenePosition | Obtain genomic positions of genes from a refGene-style... |
| E3GetJaccard | Compute Jaccard index of two vectors (size of intersection... |
| E3GetJaccardDistance | Compute a distance matrix between gene sets based on the... |
| E3GetObservedExpectedGroupFC | Produce a score based on whether a genes is consistent with... |
| E3GetOverlap | Compute overlap (number of shared elements) between two... |
| E3GetRelativeOverlap | Compute relative overlap (number of shared elements divided... |
| E3LoadExp3pGeneData | Load expression data for samples from Exp3p-like data files. |
| E3LoadGMT | Read GMT signatures from a file and produce a list of vectors... |
| E3LoadPlateConfig | Load sample information from csv files. |
| E3MakeFCSegmentation | Perform genomic segmentation. |
| E3MakeGLMs | Create GLM models linking Overlap with an expected signature... |
| E3MakeGroupCovariates | Collapse a per-sample table of covariates into a per-group... |
| E3MakeGroupSignatureScores | Average scores over several replicates to obtain one score... |
| E3MakeSampleGroups | Create a list of vectors describing how samples are related... |
| E3MakeSignatureFromScores | Create a named list with gene signatures from a matrix with... |
| E3MeasureGroupConsistency | Evaluate various metrics comparing sample and group... |
| E3PlotBasicHeat | Draw a heatmap using Rcssplot. |
| E3PlotBeforeAfter | Draw a bar-plot with two bars per label (using Rcssplot) |
| E3PlotBoxes | Draw a boxplot (using Rcssplot) |
| E3PlotClusteringDiamond | Draw a complex diagram containing a tree/diamond clustering... |
| E3PlotContourScatter | Draw a contour plot with select markers |
| E3PlotHist | Draw a histogram (using Rcssplot) |
| E3PlotLines | Draw series data as points with smoothed lines (using... |
| E3PlotScatter | Draw a scatter plot, including line of best fit, correlation... |
| E3PlotScatterBubbles | Draw a scatter plot using bubble of various sizes (using... |
| E3PlotSegmentationOverview | Draws a heatmap representation of a genomic segmentation... |
| E3PlotSmoothGenomeOverview | Draws a heatmap representation of regional genomic patterns... |
| E3PlotStimulusLegend | Draw a legend with boxes and albels (using Rcssplot) |
| E3PlotVioSet | Draw a set of violins (using Rcssplot, sm) |
| E3RescaleIntervals | Apply interval rescale factors, i.e. change low and high... |
| E3SpearmanRhoFromRanks | Compute spearman correlations using ranks |
| E3Val2Col | Convert a number into a color using transparency |
| E3ValMat2ColMat | Convert a matrix of values (range [-Inf,Inf] to colors using... |
| E3Vioplot | Draw violin onto a plot. |
| E3WriteSignatureGMT | Write signatures into gmt files (text format) |
