Analysis of cell/stimulus/gene expression data

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) |

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