Basics | Install visiumStitched | Citing visiumStitched | Packages used in this vignette | Preparing Experiment Information | Preparing Inputs to Fiji | Building a SpatialExperiment | Stitching Images with Fiji | Creating Group-Level Samples | Constructing the Object | Examining the stitched data | Stitched plotting | Defining Array Coordinates | Error metrics | Downstream applications | Conclusion | Reproducibility | Bibliography

Basics | Install qsvaR | Required knowledge | Asking for help | Citing qsvaR | qsvaR Overview | Significant Transcripts | Get Degradation Matrix | Generate principal components | Calculate Number of PCs Needed | Return qSV Matrix | Differential Expression | Conclusion | Acknowledgements | Reproducibility | Bibliography

Load data | Geometric transformations notes | A note on normalization | Merging overlapping spots