Introduction | Loading the package | Initializing the genome for transcript selection | Reading in the splicing analysis file | Additional annotation | Analyzing a specific gene | Inspecting a single gene in more detail (single record) | Finding relevant transcripts from the ENSEMBL database | Constructing the region of interest (ROI) | Finding transcripts that contain the ROI | Simulating alternatively spliced products | Simulating the outcome of exon skipping by removing an exonic region | Simulating the outcome of intron retention by inserting an intronic region | Comparing sequences before and after removal/insertion of a region | Designing primers to inspect splicing regions | Getting the DNA of the region of interest | Using Primer3 to design primers for alternative splicing identification | Checking primers coverage | Predicting PCR results using the primers | Selecting sizes relevant to splicing event (subset of getPCRsizes) | Plotting results | Session info

Preliminaries | Loading the packages | Data pre-processing | Fluorescence estimation | Reading in image/text files | Image spot estimation | Quality control (identification of outliers) | Re-estimation step (for outliers) | Final estimation | Fluorescence adjustment and estimation of cell cycle phases / pseudotime | Fluorescence adjustment on estimations from Section 2.6 | Data inspection by batch (chip) | If data consists of more than 1 chip run/batch | If data consists of a single chip run/batch | Cross-validation to assess the stability of the estimates

Introduction | Installing and loading the ssviz package | Using ssviz | Further work | References

Introduction | Installing and loading the deltaGseg package | Using deltaGseg | Appendix | References

1 Preliminaries | 2 Fluorescence estimation | 3 Adjustment and estimation of cell cycle phases / pseudotime