Man pages for ncborcherding/scRepertoire
A toolkit for single-cell immune receptor profiling
| addVariable | Adding variables after combineTCR() or combineBCR() |
| alluvialClones | Alluvial plotting for single-cell object meta data |
| clonalAbundance | Demonstrate the relative abundance of clones by group or... |
| clonalBias | Examine skew of clones towards a cluster or compartment |
| clonalCluster | Clustering adaptive receptor sequences by edit distance |
| clonalCompare | Demonstrate the difference in clonal proportions / counts... |
| clonalDiversity | Calculate the clonal diversity for samples or groupings |
| clonalHomeostasis | Examining the clonal homeostasis of the repertoire |
| clonalLength | Demonstrate the distribution of clonal length |
| clonalNetwork | Visualize clonal network along reduced dimensions |
| clonalOccupy | Visualize the number of single cells with cloneSizes by... |
| clonalOverlap | Examining the clonal overlap between groups or samples |
| clonalOverlay | Visualize distribution of clonal frequency overlaid on... |
| clonalProportion | Examining the clonal space occupied by specific clones |
| clonalQuant | Quantify the unique clones by group or sample |
| clonalRarefaction | Calculate rarefaction based on the abundance of clones |
| clonalScatter | Scatter plot comparing the clonal expansion of two samples |
| clonalSizeDistribution | Hierarchical clustering of clones using Gamma-GPD spliced... |
| combineBCR | Combining the list of B cell receptor contigs into clones |
| combineExpression | Adding clone information to a single-cell object |
| combineTCR | Combining the list of T cell receptor contigs into clones |
| contig_list | A list of 8 single-cell T cell receptor sequences runs. |
| createHTOContigList | Generate a contig list from a multiplexed experiment |
| exportClones | Exporting clones |
| getCirclize | Generate data frame to be used with circlize R package to... |
| getContigDoublets | Get Contig Doublets |
| highlightClones | Highlighting specific clones in Seurat |
| loadContigs | Loading the contigs derived from single-cell sequencing |
| mini_contig_list | Processed subset of 'contig_list' |
| percentAA | Examining the relative amino acid composition by position |
| percentGenes | Examining the VDJ gene usage across clones |
| percentKmer | Examining the relative composition of kmer motifs in clones. |
| percentVJ | Quantifying the V and J gene usage across clones |
| positionalEntropy | Examining the diversity of amino acids by position |
| positionalProperty | Examining the mean property of amino acids by position |
| scRepertoire-package | scRepertoire: A toolkit for single-cell immune receptor... |
| scRep_example | A Seurat object of 500 single T cells, |
| StartracDiversity | Startrac-based diversity indices for single-cell RNA-seq |
| subsetClones | Subset the product of combineTCR() or combineBCR() |
| vizGenes | Visualizing the distribution of gene usage |
