├── .Rbuildignore ├── .gitattributes ├── .gitignore ├── CONTRIBUTING.md ├── DESCRIPTION ├── LICENSE ├── Meta └── vignette.rds ├── NAMESPACE ├── R ├── data_simulators.R ├── func.R ├── input.R ├── rats.R └── results.R ├── README.md ├── doc ├── input.R ├── input.Rmd ├── input.html ├── output.R ├── output.Rmd ├── output.html ├── plots.R ├── plots.Rmd └── plots.html ├── inst ├── CITATION └── doc │ ├── input.R │ ├── input.Rmd │ ├── input.html │ ├── output.R │ ├── output.Rmd │ ├── output.html │ ├── plots.R │ ├── plots.Rmd │ └── plots.html ├── man ├── alloc_out.Rd ├── annot2ids.Rd ├── annot2models.Rd ├── annotation_inconsistent.Rd ├── calculate_DTU.Rd ├── call_DTU.Rd ├── denest_sleuth_boots.Rd ├── do_boot.Rd ├── dtu_plurality_summary.Rd ├── dtu_summary.Rd ├── dtu_switch_summary.Rd ├── fish4rodents.Rd ├── g.test.1.Rd ├── g.test.2.Rd ├── get_dtu_ids.Rd ├── get_plurality_ids.Rd ├── get_switch_ids.Rd ├── granges2ids.Rd ├── group_samples.Rd ├── gtf2ids.Rd ├── infer_bootnum.Rd ├── maxabs.Rd ├── parameters_are_good.Rd ├── plot_diagnostics.Rd ├── plot_gene.Rd ├── plot_overview.Rd ├── plot_shiny_volcano.Rd ├── scale_data.Rd ├── sim_boot_data.Rd ├── sim_count_data.Rd ├── structure_data.Rd └── tidy_annot.Rd ├── tests ├── test-all.R └── testthat │ ├── test.gtf │ ├── test_1_internal-structures.R │ ├── test_2_data-munging.R │ ├── test_3_input-checks.R │ ├── test_4_steps.R │ ├── test_5_output.R │ ├── test_6_reports.R │ └── test_7_extras.R └── vignettes ├── figs ├── dge-dte-dtu.jpg ├── dprop.jpg ├── fcVSdprop.jpg ├── fcvolcano.jpg ├── gvolcano.jpg ├── maxdprop.jpg ├── rats_logo.png ├── rats_workflow.jpg ├── reprod.jpg ├── reprodVSdprop.jpg └── tvolcano.jpg ├── input.R ├── input.Rmd ├── input.html ├── input.md ├── output.R ├── output.Rmd ├── output.html ├── output.md ├── plots.R ├── plots.Rmd ├── plots.html ├── plots.md └── plots_files └── figure-html ├── unnamed-chunk-3-1.png ├── unnamed-chunk-4-1.png └── unnamed-chunk-9-1.png /.Rbuildignore: 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