affycoretools           Make repetitive analyses of microarray and
                        RNA-Seq data simpler with affycoretools.
affystart               Pre-processing for Affymetrix Data
annotateEset            Method to annotate ExpressionSets automatically
dataAndHeatmapPage      A function to create an annotated HTML table
                        for all genes in a significant gene set as well
                        as a heatmap of these data.
doGlimma                A function to generate MA-plots from Glimma,
                        for all contrasts.
entrezLinks             Add links to data when using ReportingTools
fixHeaderAndGo          Fix data.frame header for use with
                        ReportingTools
geneSetPage             A function to create an HTML page for each gene
                        set, as well as the HTML pages for each
                        significant gene set.
getMainProbes           Remove control probesets from ST arrays
gsHeatmap               A function to create a simple heatmap and key.
makeGoGeneTable         Make Gene table from GO analysis results
makeGoTable             Create HTML tables for Gene Ontology (GO)
                        analyses
makeHmap                A function to create a heatmap-like object or
                        matrix of correlations between miRNA and mRNA
                        data.
makeImages              Add dotplot images
makeVenn                High-level function for making Venn diagrams
                        and outputting the results from the diagrams in
                        HTML and CSV files.
maplot                  A Function to make MA plots from all arrays.
mirna2mrna              A function to map miRNA to mRNA.
outputRomer             A function to create HTML output from the
                        results of running romer on a set of contrasts.
plotDeg                 Functions to Plot Density and RNA Degradation
                        Plots
plotPCA                 A Function to Make a PCA Plot from an
                        ExpressionSet or matrix
runRomer                A function to run the romer function on a set
                        of contrasts.
venn4Way                4-way Venn Diagrams
vennCounts2             Compute Counts for Venn Diagram
vennInLine              Generate Venn diagrams with links for Rmarkdown
                        documents
vennPage                High-level function for making Venn diagrams
                        with clickable links to HTML pages with the
                        underlying genes.
vennSelect2             Select and Output Genelists Based on Venn
                        Diagrams
writeFit                Function to output annotated fit data from
                        limma