Input | What does scMaSigPro need from a trajectory? | How do I analyse a Monocle3 trajectory? | What about cells that belong to several paths? | Raw or normalised counts? | How many cells and bins are enough? | The paths have different lengths. Does that matter? | Settings | Which bin rule should I use? | Which test should I use for the full model, chi-squared or F? | When should I turn the offset off? | How do I fit the genes in parallel? | Are the results reproducible? | Results | No gene passes. What now? | Why do my results differ from those of version 0.0.4 or the 2024 article? | I saved an object with an earlier version. Can I still use it? | How do I get the results into my SingleCellExperiment? | How long does an analysis take? | Citing scMaSigPro | Session information

The ScMaSigPro object | Two resolutions and the results | Cells and bins | The design | The results | The settings | Objects from earlier versions | Equivalence with maSigPro | A Gaussian model on microarray data | A negative binomial model on counts | What scMaSigPro adds | Session information | References

The data | Bins | The model | A polynomial in pseudotime per path | The reference path | The negative binomial distribution and theta | The offset | The link | The steps and their settings | Testing each gene | Selecting the terms | Gene lists | Influential observations | Reading the coefficients | Parallel fits | The settings against the truth | Session information | References

Introduction | Installation | The data | The workflow | Create the object | Bin the cells along pseudotime | Set up the polynomial model | Find the genes that change | Select the significant terms | List the significant genes | Plot gene trends | Cluster the trends | Get the results | Compare with the simulated truth | Session information | References

Root, link and end paths | The object | Each segment as a path | The root and the link in every path | By hand | Choosing the reference path | Session information | References

The input contract | From lineage weights | From slingshot | From a trajectory graph | From Monocle3 | Other tools | Session information | References