Package: DEXSeq 1.59.0

Overview | Preparations | Example data | Executability of the code | Alignment | Preparing the annotation | Counting reads | Building a DEXSeqDataSet | Standard analysis workflow | Loading and inspecting the example data | Normalisation | Dispersion estimation | Testing for differential exon usage | Additional technical or experimental variables | Visualization | Parallelization and large number of samples | Perform a standard differential exon usage analysis in one command | Appendix | Controlling FDR at the gene level | Preprocessing with python | Preparing the annotation file with python | Counting reads with python | Reading the data from the python ouputs into R | Preprocessing using featureCounts | Further accessors | Overlap operations | Methodological changes since publication of the paper | Requirements on GTF files | Session Information | References