Man pages for tkonopka/ExpCube
Analysis of cell/stimulus/gene expression data

E3AxesDraw axes and labels on x/y, using Rcssplot
E3CalcAcrossGroupIntervalRescaleFactorsEstimate an interval rescale factor for each feature/gene...
E3CalcWithinGroupIntervalRescaleFactorsEstimates an interval rescale factor for each feature/gene...
E3CompareSignaturesCollect metrics (Jaccard, Overlap, Fisher) describing to what...
E3CompareVectorstake two vectors A, B returns a list with elements in A only,...
E3DEscoreCompute a score summarizing a fold-change and a z-value into...
E3dist.euclideanCompute euclidean distances between all pairs of samples
E3dist.spearmanCompute spearman pseudo-distances between all pairs of...
E3DrawMarkerLegendDraw a vertical legend with markers (circles, boxes, and...
E3DrawScaleLegendDraw a vertical recrangle with a color scale and labels
E3GetDEScoresCompute DE scores for a single sample.
E3GetExpressedGenesDetermine genes that are expressed in a dataset. Expressed...
E3GetFisherPCompute fisher p-value: selection of two vectors from a...
E3GetGenePositionObtain genomic positions of genes from a refGene-style...
E3GetJaccardCompute Jaccard index of two vectors (size of intersection...
E3GetJaccardDistanceCompute a distance matrix between gene sets based on the...
E3GetObservedExpectedGroupFCProduce a score based on whether a genes is consistent with...
E3GetOverlapCompute overlap (number of shared elements) between two...
E3GetRelativeOverlapCompute relative overlap (number of shared elements divided...
E3LoadExp3pGeneDataLoad expression data for samples from Exp3p-like data files.
E3LoadGMTRead GMT signatures from a file and produce a list of vectors...
E3LoadPlateConfigLoad sample information from csv files.
E3MakeFCSegmentationPerform genomic segmentation.
E3MakeGLMsCreate GLM models linking Overlap with an expected signature...
E3MakeGroupCovariatesCollapse a per-sample table of covariates into a per-group...
E3MakeGroupSignatureScoresAverage scores over several replicates to obtain one score...
E3MakeSampleGroupsCreate a list of vectors describing how samples are related...
E3MakeSignatureFromScoresCreate a named list with gene signatures from a matrix with...
E3MeasureGroupConsistencyEvaluate various metrics comparing sample and group...
E3PlotBasicHeatDraw a heatmap using Rcssplot.
E3PlotBeforeAfterDraw a bar-plot with two bars per label (using Rcssplot)
E3PlotBoxesDraw a boxplot (using Rcssplot)
E3PlotClusteringDiamondDraw a complex diagram containing a tree/diamond clustering...
E3PlotContourScatterDraw a contour plot with select markers
E3PlotHistDraw a histogram (using Rcssplot)
E3PlotLinesDraw series data as points with smoothed lines (using...
E3PlotScatterDraw a scatter plot, including line of best fit, correlation...
E3PlotScatterBubblesDraw a scatter plot using bubble of various sizes (using...
E3PlotSegmentationOverviewDraws a heatmap representation of a genomic segmentation...
E3PlotSmoothGenomeOverviewDraws a heatmap representation of regional genomic patterns...
E3PlotStimulusLegendDraw a legend with boxes and albels (using Rcssplot)
E3PlotVioSetDraw a set of violins (using Rcssplot, sm)
E3RescaleIntervalsApply interval rescale factors, i.e. change low and high...
E3SpearmanRhoFromRanksCompute spearman correlations using ranks
E3Val2ColConvert a number into a color using transparency
E3ValMat2ColMatConvert a matrix of values (range [-Inf,Inf] to colors using...
E3VioplotDraw violin onto a plot.
E3WriteSignatureGMTWrite signatures into gmt files (text format)
tkonopka/ExpCube documentation built on May 27, 2017, 9:43 a.m.