Man pages for JuanXie19/LRT
LRT (Lineage estimation by integrative analysis of single-cell RNA-seq and TCR-seq data)
| clonalDiversity | Examine the clonal diversity of samples |
| clonalOverlap | repertorie analysis functions used for shinyClone modified... |
| clonalProportion | Examining the clonal space occupied by specific clonotypes |
| CombinedDataSet-class | Class 'CombinedDataSet' |
| diversityCall | Calculating diversity using Vegan R package |
| expression2List | Allows users to take the meta data in CombinedDataSet and... |
| expression2List_seurat | Allows users to take the meta data in Seurat and place it... |
| getCirclize | a function to prepare input for chord diagram |
| getClonotypeLineages | Infer clonotype lineage structure from 'CombinedDatSet' |
| getCombinedDataSet | Initialize an object of class 'CombinedDataSet' |
| getCombinedDataSet-data.frame-Seurat-method | Combine scTCR-seq and scRNA-seq data |
| getOverallTrajectory-CombinedDataSet-method | get Overall Trajectory |
| getShinyInput | prepare the input for shiny apps |
| getTCRs | extract the TCR information fomr CombinedDataSet |
| grabMeta | This is to grab the meta data from a CombinedDataSet object |
| grabMeta_seurat | This is to grab the meta data from a seurat object |
| jaccardIndex | Calculate the Jaccard Similarity Index for Overlap Analysis |
| list.input.return | return a list |
| lrtLineages | extract the inferred clonotype lineages |
| lrtParams | extract the parameters used when estimating lineages |
| morisitaIndex | calculate the Morisita index for Overlap Analysis |
| occupiedscRepertoire | Visualize the number of single cells with clonotype... |
| overlapIndex | Calculate the Overlap Coefficient for Overlap Analysis |
| reducedDim | extract the UMAP coordinates from CombinedDatSet |
| seuratClusterLabels | extract the seurat cell cluster labels from CombinedDataSet |
| shinyClone | Explanatory analysis of clonotype |
| shinyClust | cluster inferred clonotype trajectories |
| TrajectoryDataSet-class | Class 'TrajectoryDataSet' |
