Man pages for CellaRepertorium
Data structures, clustering and testing for single cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
| canonicalize_cell | Find a canonical contig to represent a cell |
| canonicalize_cluster | Find a canonical contig to represent a cluster |
| cash-ContigCellDB-method | Access public members of ContigCellDB object. |
| ccdb_ex | A preconstructed 'ContigClusterDB' from the 'contigs_qc' data |
| ccdb_join | Join dataframe or SingleCellExperiment object with... |
| cdhit | R interface to CDHIT/CDHITest |
| cdhit_ccdb | Use 'cdhit()' to cluster a 'ContigCellDB()' |
| cluster_filterset | A filtration of clusters |
| cluster_germline | Cluster contigs by germline properties |
| cluster_logistic_test | Test clusters for differential usage |
| cluster_permute_test | Tests for independence between labels and covariates using... |
| cluster_plot | Make a plot showing properties of the clustering |
| ContigCellDB-fun | Construct a ContigCellDB |
| contigs_qc | Filtered and annotated contigs of TCR from mice |
| crosstab_by_celltype | Count contig UMIs by celltype |
| dot-cluster_permute_test | Cell permutation tests (internal) |
| entropy | Calculate the entropy of a vector |
| enumerate_pairing | Categorize the pairing present in a cell |
| equalize_ccdb | Take the intersection of keys in tables in 'x' |
| fancy_name_contigs | Generate a legible name for a series of contigs |
| fine_clustering | Perform additional clustering of sequences within groups |
| fine_cluster_seqs | Calculate distances and perform hierarchical clustering on a... |
| generate_pseudobulk | Generate "pseudobulk" data from a 'ContigCellDB' |
| guess_celltype | Guess the cell type of a contig from the chain ID |
| hushWarning | Selectively muffle warnings based on output |
| left_join_warn | Perform a 'dplyr::left_join()' but check for non-key... |
| map_axis_labels | Color axis labels |
| mutate_cdb | Create new or update existing columns of 'ContigCellDB'... |
| pairing_tables | Generate a list of tables representing clusters paired in... |
| purity | Calculate number of cluster-subject singletons for the... |
| rank_prevalence_ccdb | Rank contigs, per cell, by experiment-wide prevalence of... |
| rbind-ContigCellDB-method | Combine 'ContigCellDB' along rows (contigs, cells or... |
| split_cdb | Split into a list of 'ContigCellDB()' by named fields |
| sub-sub-ContigCellDB-character-missing-method | 'data.frame'-like mutation/accessor generics for... |
