├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ ├── check-bioc.yaml │ ├── check-standard.yaml │ ├── pkgdown.yaml │ └── test-coverage.yaml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── calc-diversity.R ├── calc-frequency.R ├── calc-gene-usage.R ├── calc-similarity.R ├── cluster-seqs.R ├── data.R ├── djvdj-global.R ├── djvdj-package.R ├── filter-vdj.R ├── import-vdj.R ├── mutate-vdj.R ├── plotting-labels.R ├── plotting-utils.R ├── plotting.R ├── utils-tidy-eval.R └── utils.R ├── README.Rmd ├── README.md ├── codecov.yml ├── data-raw ├── splenocytes.R └── tiny.R ├── data ├── splen_meta.rda ├── tiny_sce.rda └── vdj_sce.rda ├── djvdj.Rproj ├── inst └── extdata │ └── splen │ ├── BL6_BCR │ ├── airr_rearrangement.tsv.gz │ ├── concat_ref.bam │ └── filtered_contig_annotations.csv.gz │ ├── BL6_GEX │ └── filtered_feature_bc_matrix │ │ ├── barcodes.tsv.gz │ │ ├── features.tsv.gz │ │ └── matrix.mtx.gz │ ├── BL6_TCR │ ├── airr_rearrangement.tsv.gz │ ├── concat_ref.bam │ └── filtered_contig_annotations.csv.gz │ ├── MD4_BCR │ ├── airr_rearrangement.tsv.gz │ ├── concat_ref.bam │ └── filtered_contig_annotations.csv.gz │ ├── MD4_GEX │ └── filtered_feature_bc_matrix │ │ ├── barcodes.tsv.gz │ │ ├── features.tsv.gz │ │ └── matrix.mtx.gz │ └── MD4_TCR │ ├── airr_rearrangement.tsv.gz │ ├── concat_ref.bam │ └── filtered_contig_annotations.csv.gz ├── man ├── calc_diversity.Rd ├── calc_frequency.Rd ├── calc_gene_pairs.Rd ├── calc_gene_usage.Rd ├── calc_mds.Rd ├── calc_similarity.Rd ├── cluster_sequences.Rd ├── define_clonotypes.Rd ├── djvdj-package.Rd ├── djvdj_theme.Rd ├── fetch_vdj.Rd ├── figures │ ├── README-usage-1.png │ ├── djvdj-logo-2.png │ ├── djvdj-logo-dark-3.png │ ├── djvdj-logo.png │ └── logo.png ├── filter_vdj.Rd ├── import_vdj.Rd ├── mutate_meta.Rd ├── mutate_vdj.Rd ├── plot_clone_frequency.Rd ├── plot_diversity.Rd ├── plot_frequency.Rd ├── plot_gene_pairs.Rd ├── plot_gene_usage.Rd ├── plot_mds.Rd ├── plot_motifs.Rd ├── plot_numerical.Rd ├── plot_rarefaction.Rd ├── plot_scatter.Rd ├── plot_similarity.Rd ├── splen_meta.Rd ├── summarize_vdj.Rd ├── tidyeval.Rd ├── tiny_sce.Rd └── vdj_sce.Rd ├── pkgdown ├── _pkgdown.yml ├── extra.css └── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ └── favicon.ico ├── tests ├── testthat.R └── testthat │ ├── test-calc-diversity.R │ ├── test-calc-frequency.R │ ├── test-calc-gene-usage.R │ ├── test-calc-similarity.R │ ├── test-cluster-seqs.R │ ├── test-filter-vdj.R │ ├── test-import-vdj.R │ ├── test-mutate-vdj.R │ ├── test-plots.R │ └── test-utils.R └── vignettes ├── clustering.Rmd ├── diversity.Rmd ├── frequency.Rmd ├── gene-usage.Rmd ├── import.Rmd ├── mutate.Rmd ├── plotting.Rmd └── similarity.Rmd /.Rbuildignore: 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