├── .Rbuildignore ├── .coveralls.yml ├── .github ├── .gitignore ├── ISSUE_TEMPLATE │ └── bug_report.md └── workflows │ └── rworkflows.yml ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── NAMESPACE ├── R ├── attach.R ├── data.R ├── dplyr_methods.R ├── ggplot2_methods.R ├── methods.R ├── methods_DEPRECATED.R ├── pillar_utilities.R ├── plotly_methods.R ├── print_method.R ├── tibble_methods.R ├── tidyr_methods.R ├── utilities.R ├── utils-pipe.R └── zzz.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── codecov.yml ├── data ├── cell_type_df.rda └── pbmc_small_nested_interactions.rda ├── dev ├── Thumbs.db ├── code_comparison.Rmd ├── gating.png ├── plot_seurat_structure.R ├── plotly.png ├── seurat_structure.png ├── seurat_structure_square.png ├── test_scrna_for_tidyseurat.rdata ├── tidyseurat_structure.png ├── tidyseurat_structure_square.png ├── use_cases_BioCAsia2021.R ├── workflow_article.R ├── workflow_create_integrated_pbmc.R └── workflow_figures.R ├── inst ├── CITATION ├── NEWS.rd ├── Thumbs.db ├── logo.png ├── logo.svg └── logo_source_no_outline.svg ├── man ├── add_class.Rd ├── aggregate_cells.Rd ├── arrange.Rd ├── as_tibble.Rd ├── bind_rows.Rd ├── cell_type_df.Rd ├── count.Rd ├── distinct.Rd ├── drop_class.Rd ├── extract.Rd ├── figures │ ├── .DS_Store │ ├── lifecycle-archived.svg │ ├── lifecycle-defunct.svg │ ├── lifecycle-deprecated.svg │ ├── lifecycle-experimental.svg │ ├── lifecycle-maturing.svg │ ├── lifecycle-questioning.svg │ ├── lifecycle-soft-deprecated.svg │ ├── lifecycle-stable.svg │ ├── lifecycle-superseded.svg │ ├── logo_interaction-01.png │ ├── markers_v4-1.png │ ├── pc_plot-1.png │ ├── plot1-1.png │ ├── plot2-1.png │ ├── plotly.png │ ├── unnamed-chunk-12-1.png │ ├── unnamed-chunk-14-1.png │ ├── unnamed-chunk-15-1.png │ ├── unnamed-chunk-16-1.png │ ├── unnamed-chunk-17-1.png │ ├── unnamed-chunk-18-1.png │ ├── unnamed-chunk-19-1.png │ ├── unnamed-chunk-20-1.png │ └── unnamed-chunk-22-1.png ├── filter.Rd ├── formatting.Rd ├── fragments │ ├── intro.Rmd │ └── intro_files │ │ └── figure-html │ │ ├── markers_v4-1.png │ │ ├── pc_plot-1.png │ │ ├── plot1-1.png │ │ ├── plot2-1.png │ │ └── unnamed-chunk-9-1.png ├── full_join.Rd ├── get_abundance_sc_long.Rd ├── get_abundance_sc_wide.Rd ├── ggplot.Rd ├── glimpse.Rd ├── group_by.Rd ├── group_split.Rd ├── inner_join.Rd ├── join_features.Rd ├── join_transcripts.Rd ├── left_join.Rd ├── mutate.Rd ├── nest.Rd ├── pbmc_small_nested_interactions.Rd ├── pipe.Rd ├── pivot_longer.Rd ├── plotly.Rd ├── pull.Rd ├── quo_names.Rd ├── rename.Rd ├── return_arguments_of.Rd ├── right_join.Rd ├── rowwise.Rd ├── sample_n.Rd ├── select.Rd ├── separate.Rd ├── slice.Rd ├── summarise.Rd ├── tbl_format_header.Rd ├── tidy.Rd ├── unite.Rd └── unnest.Rd ├── tests ├── testthat.R └── testthat │ ├── test-dplyr.R │ ├── test-ggplotly_methods.R │ ├── test-methods.R │ ├── test-pillar.R │ ├── test-print.R │ ├── test-tidyr.R │ └── test-utilities.R └── vignettes ├── figures_article.Rmd ├── introduction.Rmd └── tidyseurat.bib 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