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