Man pages for rnabioco/AVIDtools
A collection of single-cell V(D)J tools
| calc_diversity | Calculate repertoire diversity |
| calc_frequency | Calculate frequency of cell groups present in object |
| calc_gene_pairs | Calculate paired usage of V(D)J segments across chains |
| calc_gene_usage | Calculate V(D)J segment usage |
| calc_mds | Perform multidimensional scaling |
| calc_similarity | Calculate repertoire similarity |
| cluster_sequences | Cluster cells based on CDR3 sequences |
| define_clonotypes | Define clonotypes based on V(D)J data |
| djvdj-package | djvdj: A collection of single-cell V(D)J tools |
| djvdj_theme | Theme for djvdj plotting functions |
| fetch_vdj | Fetch V(D)J data from object |
| filter_vdj | Filter V(D)J data in object |
| import_vdj | Import V(D)J data |
| mutate_meta | Modify object meta.data |
| mutate_vdj | Modify V(D)J data in object |
| plot_clone_frequency | Plot clonotype frequency |
| plot_diversity | Plot repertoire diversity |
| plot_frequency | Plot frequency of cell groups present in object |
| plot_gene_pairs | Plot paired usage of V(D)J segments across chains |
| plot_gene_usage | Plot V(D)J segment usage |
| plot_mds | Create MDS plot |
| plot_motifs | Plot CDR3 sequence motifs |
| plot_numerical | Plot numerical single-cell data |
| plot_rarefaction | Plot rarefaction curves |
| plot_scatter | Create 2D scatter plot |
| plot_similarity | Plot repertoire similarity |
| splen_meta | Meta data for downsampled splenocyte data |
| summarize_vdj | Summarize V(D)J data for each cell |
| tidyeval | Tidy eval helpers |
| tiny_sce | A tiny SingleCellExperiment object |
| vdj_sce | A tiny SingleCellExperiment object with V(D)J data |
