Load the required libraries | Load data | Filter the data | Milo object and neighbourhood graph construction | Construct UMAP on milo neighbor graph | Construct pseudobulked VDJ feature space | TCR trajectory inference using Absorbing Markov Chain | Define root and branch tips | Construct diffusion map | Compute diffussion pseudotime on diffusion map | Markov chain construction on the pseudobulk VDJ feature space | Visualising branch probabilities | Transfer | Project pseudobulk data to each cell | Visualise the trajectory data on a per cell basis | Session info

Foreword | Installation | Bioconductor | Development version (GitHub) | Usage | Load the required libraries | Load the demo data | Use scRepertoire to load the VDJ data | Merging VDJ data with gene expression data | Initiate dandelionR workflow | Milo object and neighbourhood graph construction | Construct UMAP on milo neighbor graph | Construct pseudobulked VDJ feature space | TCR trajectory inference using Absorbing Markov Chain | Define root and branch tips | Construct diffusion map | Compute diffusion pseudotime on diffusion map | Markov chain construction on the pseudobulk VDJ feature space | Visualising branch probabilities | Transfer | Project pseudobulk data to each cell | Visualise the trajectory data on a per cell basis | Session info

Foreword | Installing slinshot | Load the required libraries and data | Setup the data as per the other vignettes | Milo object and neighbourhood graph construction | Construct UMAP on milo neighbor graph | Construct pseudobulked VDJ feature space | TCR trajectory inference using Slingshot | input | run slingshot | Visualization | Transfer | Project pseudobulk data to each cell | Visualise the trajectory data on a per cell basis | Session info