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| SARTools-package | Statistical Analysis of RNA-Seq Tools |
| barplotNull | Percentage of null counts per sample |
| barplotTotal | Total number of reads per sample |
| BCVPlot | BCV plot (for edgeR dispersions) |
| checkParameters.DESeq2 | Check the parameters (when using DESeq2) |
| checkParameters.edgeR | Check the parameters (when using edgeR) |
| clusterPlot | Clustering of the samples |
| countsBoxplots | Box-plots of (normalized) counts distribution per sample |
| densityPlot | Density plot of all samples |
| descriptionPlots | Description plots of the counts |
| diagSizeFactorsPlots | Assess the estimations of the size factors |
| dispersionsPlot | Plots about DESeq2 dispersions |
| exploreCounts | Explore counts structure |
| exportResults.DESeq2 | Export results for DESeq2 analyses |
| exportResults.edgeR | Export results for edgeR analyses |
| loadCountData | Load count files |
| loadTargetFile | Load target file |
| majSequences | Most expressed sequences per sample |
| MAPlot | MA-plots |
| MDSPlot | MDS plot (for edgeR objects) |
| nDiffTotal | Number of differentially expressed features per comparison |
| pairwiseScatterPlots | Scatter plots for pairwise comparaisons of log counts |
| PCAPlot | PCA of samples (if use of DESeq2) |
| rawpHist | Histograms of raw p-values |
| removeNull | Remove features with null counts in all samples |
| run.DESeq2 | Wrapper to run DESeq2 |
| run.edgeR | Wrapper to run edgeR |
| SERE | Pairwise SERE for two samples |
| summarizeResults.DESeq2 | Summarize DESeq2 analysis |
| summarizeResults.edgeR | Summarize edgeR analysis |
| tabIndepFiltering | Table of the number of features discarded by the independent filtering (if use of DESeq2) |
| tabSERE | SERE statistics for several samples |
| volcanoPlot | Volcano plots |
| writeReport.DESeq2 | Write HTML report for DESeq2 analyses |
| writeReport.edgeR | Write HTML report for edgeR analyses |