Overview of citcdf | Main user functions | Inputs | Testing a single hypothesis | The data | Asymptotic test with cit_asymp() | Permutation test with cit_perm() | Visualization | Testing many outcomes with cit_multi() | scRNA-seq data | Asymptotic analysis | Permutation analysis | Practical considerations | Session information | References

Introduction to cytoftree | Data transformation | Binary tree construction | Post-hoc annotation | Influenza vaccine response dataset analysis with cytoftree | Data preparation | CytofTree function | High dimensional issues | Annotation function | RetrievePops : providing informations for particular sub-populations | Proportions comparison between manual and automatic gating

Introduction to cytometree | Binary tree construction | Post-hoc annotation | Examples of analysis with cytometree | Diffuse large B-cell lymphoma dataset with 3 markers | Automatic gating step | Post-processing annotation of automatically gated subpopulations | Comparison between manual and automatic gating | PBMC sample from the Human Immunology Project | Semi-supervised gating

Overview of TcGSA | Getting started using TcGSA | Gene set object | Download gmts from Hejblum et al., 2015 | Self-built gmt | Gene expression matrix | Design data matrix | How to use TcGSA for one treatment group ? | Data preparation | Import of data files | Likelihood ratios test | Graphical outputs | How to use TcGSA for several treatment group ? | Likelihood ratio tests | Graphical outputs for significant gene sets | Make clusters from tcgsa object | Heatmap of significant gene sets | References | Appendix | GEOquery package

Introduction | Analysis of HIPC data | Data load | Computation of the benchmark class proportions for target data | CytOpT | Optimization | Results | Performance evaluation