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

Overview of dearseq | Using dearseq for a gene-wise analysis | Getting started using dear_seq() | An example analysis | Data preparation | Design data matrix | Gene expression matrix | Identifying differentially expressed genes (DEG) from dearseq variance component score test | Using gene expression matrix of raw counts | Using dearseq for gene-set analysis | Bibliography | Appendix | GEOquery package | readxl | Session Info