| affycoretools | Make repetitive analyses of microarray and RNA-Seq data simpler with affycoretools. |
| affyLinks | Add links to data when using ReportingTools |
| affystart | Pre-processing for Affymetrix Data |
| annotateEset | Method to annotate ExpressionSets automatically |
| annotateEset-method | 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. |
| ensemblLinks | Add links to data when using ReportingTools |
| 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 |
| goLinks | Add links to data when using ReportingTools |
| 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. |
| makeVenn-method | 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. |
| nuccoreLinks | Add links to data when using ReportingTools |
| outputRomer | A function to create HTML output from the results of running romer on a set of contrasts. |
| outputRomer-method | 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 |
| plotHist | Functions to Plot Density and RNA Degradation Plots |
| plotPCA | A Function to Make a PCA Plot from an ExpressionSet or matrix |
| plotPCA-method | 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. |
| runRomer-method | 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 |