| affycoretools | Make repetitive analyses of microarray and RNA-Seq data... |
| affycoretools-defunct | Defunct functions in package '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... |
| doGlimma | A function to generate MA-plots from Glimma, for all... |
| 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... |
| getCols | Correct Ordering of Contrasts |
| getMainProbes | Remove control probesets from ST arrays |
| gsHeatmap | A function to create a simple heatmap and key. |
| intNames | Create Names for Venn Diagram Intersections |
| make.cl | A Function to Make a Classlabel Vector for Plotting |
| 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... |
| makeImages | Add dotplot images |
| makeIndices | Create Indices for Venn Diagrams |
| makeVenn | High-level function for making Venn diagrams and outputting... |
| 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... |
| pca.legend | A Function to Automagically Place a Legend in a PCA Plot |
| 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. |
| tableFilt | Filter a topTable object |
| 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... |
| vennSelect2 | Select and Output Genelists Based on Venn Diagrams |
| writeFit | Function to output annotated fit data from limma |
