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SampleInfo

List sample information and perform statistics

SeuratPreparing

Load, prepare and apply QC to data, using `Seurat`

ClusterMarkersOfAllCells

Markers for clusters of all cells.

TopExpressingGenesOfAllCells

Top expressing genes for clusters of all cells.

TCellSelection

Separate T and non-T cells and select T cells.

ClusterMarkers

Markers for clusters of all or selected T cells.

TopExpressingGenes

Top expressing genes for clusters of all or selected T cells.

TCRClusterStats

Statistics of TCR clusters, generated by `TCRClustering`.

TESSA

Tessa is a Bayesian model to integrate T cell receptor (TCR) sequence profiling with transcriptomes of T cells.

SeuratClusterStats

Statistics of the clustering.

Immunarch

Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

RadarPlots

Radar plots for cell proportion in different clusters.

CloneResidency

Identification of clone residency

ScFGSEA

Gene set enrichment analysis for cells in different groups using `fgsea`

MarkersFinder

Find markers between different groups of cells

MetaMarkers

Find markers between three or more groups of cells, using one-way ANOVA or Kruskal-Wallis test.

CellsDistribution

Distribution of cells (i.e. in a TCR clone) from different groups for each cluster

CDR3AAPhyschem

CDR3 AA physicochemical feature analysis