Man pages for rnabioco/AVIDtools
A collection of single-cell V(D)J tools

calc_diversityCalculate repertoire diversity
calc_frequencyCalculate frequency of cell groups present in object
calc_gene_pairsCalculate paired usage of V(D)J segments across chains
calc_gene_usageCalculate V(D)J segment usage
calc_mdsPerform multidimensional scaling
calc_similarityCalculate repertoire similarity
cluster_sequencesCluster cells based on CDR3 sequences
define_clonotypesDefine clonotypes based on V(D)J data
djvdj-packagedjvdj: A collection of single-cell V(D)J tools
djvdj_themeTheme for djvdj plotting functions
fetch_vdjFetch V(D)J data from object
filter_vdjFilter V(D)J data in object
import_vdjImport V(D)J data
mutate_metaModify object meta.data
mutate_vdjModify V(D)J data in object
plot_clone_frequencyPlot clonotype frequency
plot_diversityPlot repertoire diversity
plot_frequencyPlot frequency of cell groups present in object
plot_gene_pairsPlot paired usage of V(D)J segments across chains
plot_gene_usagePlot V(D)J segment usage
plot_mdsCreate MDS plot
plot_motifsPlot CDR3 sequence motifs
plot_numericalPlot numerical single-cell data
plot_rarefactionPlot rarefaction curves
plot_scatterCreate 2D scatter plot
plot_similarityPlot repertoire similarity
splen_metaMeta data for downsampled splenocyte data
summarize_vdjSummarize V(D)J data for each cell
tidyevalTidy eval helpers
tiny_sceA tiny SingleCellExperiment object
vdj_sceA tiny SingleCellExperiment object with V(D)J data
rnabioco/AVIDtools documentation built on Oct. 28, 2023, 10:23 a.m.