Files in ScialdoneLab/MitoHEAR
Quantification of Mitochondrial DNA Heteroplasmy

.DS_Store
.Rbuildignore
.Rhistory
.Rproj.user/E8D86276/cpp-definition-cache
.Rproj.user/E8D86276/pcs/debug-breakpoints.pper
.Rproj.user/E8D86276/pcs/files-pane.pper
.Rproj.user/E8D86276/pcs/source-pane.pper
.Rproj.user/E8D86276/pcs/windowlayoutstate.pper
.Rproj.user/E8D86276/pcs/workbench-pane.pper
.Rproj.user/E8D86276/persistent-state
.Rproj.user/E8D86276/rmd-outputs
.Rproj.user/E8D86276/saved_source_markers
.Rproj.user/E8D86276/sources/prop/125368D8
.Rproj.user/E8D86276/sources/prop/12BD479B
.Rproj.user/E8D86276/sources/prop/1E82D814
.Rproj.user/E8D86276/sources/prop/1FBB2082
.Rproj.user/E8D86276/sources/prop/2BB8D447
.Rproj.user/E8D86276/sources/prop/30EB1D02
.Rproj.user/E8D86276/sources/prop/30F76B8C
.Rproj.user/E8D86276/sources/prop/3C238F12
.Rproj.user/E8D86276/sources/prop/3E0249A9
.Rproj.user/E8D86276/sources/prop/3E3698EB
.Rproj.user/E8D86276/sources/prop/4003E84E
.Rproj.user/E8D86276/sources/prop/4D4A84DF
.Rproj.user/E8D86276/sources/prop/50B84D5A
.Rproj.user/E8D86276/sources/prop/53AF3D47
.Rproj.user/E8D86276/sources/prop/5428C311
.Rproj.user/E8D86276/sources/prop/5445F644
.Rproj.user/E8D86276/sources/prop/59294C7B
.Rproj.user/E8D86276/sources/prop/59CB0B37
.Rproj.user/E8D86276/sources/prop/5E58D96A
.Rproj.user/E8D86276/sources/prop/5FF02BF0
.Rproj.user/E8D86276/sources/prop/61FD1F4E
.Rproj.user/E8D86276/sources/prop/6288DDDE
.Rproj.user/E8D86276/sources/prop/6A384053
.Rproj.user/E8D86276/sources/prop/6C1E98CC
.Rproj.user/E8D86276/sources/prop/6C9A5FBA
.Rproj.user/E8D86276/sources/prop/71DA7733
.Rproj.user/E8D86276/sources/prop/776AC784
.Rproj.user/E8D86276/sources/prop/7E7CB712
.Rproj.user/E8D86276/sources/prop/84E23EFE
.Rproj.user/E8D86276/sources/prop/9C1396CA
.Rproj.user/E8D86276/sources/prop/A7BCE379
.Rproj.user/E8D86276/sources/prop/AA482005
.Rproj.user/E8D86276/sources/prop/AABB5C9B
.Rproj.user/E8D86276/sources/prop/C31536D2
.Rproj.user/E8D86276/sources/prop/CE8388E3
.Rproj.user/E8D86276/sources/prop/D2BFD606
.Rproj.user/E8D86276/sources/prop/D6D3496D
.Rproj.user/E8D86276/sources/prop/DB3B176
.Rproj.user/E8D86276/sources/prop/DB49F211
.Rproj.user/E8D86276/sources/prop/F385BBB6
.Rproj.user/E8D86276/sources/prop/FFEC4CAD
.Rproj.user/E8D86276/sources/prop/INDEX
.Rproj.user/shared/notebooks/BBEEFDB4-heteroplasmy_second_part/1/E8D86276D68A918B/chunks.json
.Rproj.user/shared/notebooks/BBEEFDB4-heteroplasmy_second_part/1/s/chunks.json
.Rproj.user/shared/notebooks/patch-chunk-names
.Rproj.user/shared/notebooks/paths
.gitignore
DESCRIPTION
Draft/docs/img/paper_fig_1.png
Draft/docs/img/paper_fig_2.png
Draft/docs/img/paper_fig_3.png
Draft/paper.bib
Draft/paper.md LICENSE.md
MitoHEAR.Rproj
NAMESPACE
R/.Rhistory
R/get_heteroplasmy.R R/get_raw_counts_allele.R R/lineage_tracing.R R/other_functions.R R/plotting_functions.R R/statistical_test.R R/utils.R README.md
docs/404.html
docs/LICENSE.html
docs/articles/Ludwig_et_al_example_notebook.html
docs/articles/Ludwig_et_al_example_notebook_files/figure-html/unnamed-chunk-10-1.png
docs/articles/Ludwig_et_al_example_notebook_files/figure-html/unnamed-chunk-10-2.png
docs/articles/Ludwig_et_al_example_notebook_files/figure-html/unnamed-chunk-10-3.png
docs/articles/Ludwig_et_al_example_notebook_files/figure-html/unnamed-chunk-10-4.png
docs/articles/Ludwig_et_al_example_notebook_files/figure-html/unnamed-chunk-12-1.png
docs/articles/Ludwig_et_al_example_notebook_files/figure-html/unnamed-chunk-14-1.png
docs/articles/Ludwig_et_al_example_notebook_files/figure-html/unnamed-chunk-15-1.png
docs/articles/Ludwig_et_al_example_notebook_files/figure-html/unnamed-chunk-15-2.png
docs/articles/Ludwig_et_al_example_notebook_files/figure-html/unnamed-chunk-15-3.png
docs/articles/Ludwig_et_al_example_notebook_files/figure-html/unnamed-chunk-15-4.png
docs/articles/Ludwig_et_al_example_notebook_files/figure-html/unnamed-chunk-15-5.png
docs/articles/Ludwig_et_al_example_notebook_files/figure-html/unnamed-chunk-15-6.png
docs/articles/Ludwig_et_al_example_notebook_files/figure-html/unnamed-chunk-26-1.png
docs/articles/Ludwig_et_al_example_notebook_files/figure-html/unnamed-chunk-26-2.png
docs/articles/Ludwig_et_al_example_notebook_files/figure-html/unnamed-chunk-26-3.png
docs/articles/Ludwig_et_al_example_notebook_files/figure-html/unnamed-chunk-26-4.png
docs/articles/Ludwig_et_al_example_notebook_files/figure-html/unnamed-chunk-29-1.png
docs/articles/Ludwig_et_al_example_notebook_files/figure-html/unnamed-chunk-39-1.png
docs/articles/Ludwig_et_al_example_notebook_files/figure-html/unnamed-chunk-40-1.png
docs/articles/Ludwig_et_al_example_notebook_files/figure-html/unnamed-chunk-40-2.png
docs/articles/Ludwig_et_al_example_notebook_files/figure-html/unnamed-chunk-40-3.png
docs/articles/Ludwig_et_al_example_notebook_files/figure-html/unnamed-chunk-40-4.png
docs/articles/cell_competition_bulk_data_mt_example_notebook.html
docs/articles/cell_competition_bulk_data_mt_example_notebook_files/figure-html/unnamed-chunk-12-1.png
docs/articles/cell_competition_bulk_data_mt_example_notebook_files/figure-html/unnamed-chunk-12-2.png
docs/articles/cell_competition_bulk_data_mt_example_notebook_files/figure-html/unnamed-chunk-12-3.png
docs/articles/cell_competition_bulk_data_mt_example_notebook_files/figure-html/unnamed-chunk-12-4.png
docs/articles/cell_competition_bulk_data_mt_example_notebook_files/figure-html/unnamed-chunk-13-1.png
docs/articles/cell_competition_bulk_data_mt_example_notebook_files/figure-html/unnamed-chunk-13-2.png
docs/articles/cell_competition_bulk_data_mt_example_notebook_files/figure-html/unnamed-chunk-14-1.png
docs/articles/cell_competition_bulk_data_mt_example_notebook_files/figure-html/unnamed-chunk-15-1.png
docs/articles/cell_competition_bulk_data_mt_example_notebook_files/figure-html/unnamed-chunk-15-2.png
docs/articles/cell_competition_bulk_data_mt_example_notebook_files/figure-html/unnamed-chunk-16-1.png
docs/articles/cell_competition_mt_example_notebook.html
docs/articles/cell_competition_mt_example_notebook_files/figure-html/unnamed-chunk-15-1.png
docs/articles/cell_competition_mt_example_notebook_files/figure-html/unnamed-chunk-15-2.png
docs/articles/cell_competition_mt_example_notebook_files/figure-html/unnamed-chunk-15-3.png
docs/articles/cell_competition_mt_example_notebook_files/figure-html/unnamed-chunk-15-4.png
docs/articles/cell_competition_mt_example_notebook_files/figure-html/unnamed-chunk-18-1.png
docs/articles/cell_competition_mt_example_notebook_files/figure-html/unnamed-chunk-20-1.png
docs/articles/cell_competition_mt_example_notebook_files/figure-html/unnamed-chunk-20-2.png
docs/articles/cell_competition_mt_example_notebook_files/figure-html/unnamed-chunk-22-1.png
docs/articles/cell_competition_mt_example_notebook_files/figure-html/unnamed-chunk-23-1.png
docs/articles/cell_competition_mt_example_notebook_files/figure-html/unnamed-chunk-23-2.png
docs/articles/cell_competition_mt_example_notebook_files/figure-html/unnamed-chunk-8-1.png
docs/articles/cell_competition_mt_example_notebook_files/figure-html/unnamed-chunk-9-1.png
docs/articles/index.html
docs/articles/lineage_tracing_example_notebook.html
docs/articles/lineage_tracing_example_notebook_files/figure-html/unnamed-chunk-13-1.png
docs/articles/lineage_tracing_example_notebook_files/figure-html/unnamed-chunk-14-1.png
docs/articles/lineage_tracing_example_notebook_files/figure-html/unnamed-chunk-14-2.png
docs/articles/lineage_tracing_example_notebook_files/figure-html/unnamed-chunk-14-3.png
docs/articles/lineage_tracing_example_notebook_files/figure-html/unnamed-chunk-14-4.png
docs/articles/lineage_tracing_example_notebook_files/figure-html/unnamed-chunk-20-1.png
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/choose_features_clustering.html
docs/reference/clustering_angular_distance.html
docs/reference/detect_insertion.html
docs/reference/dpt_test.html
docs/reference/figures/paper_fig_1.png
docs/reference/figures/paper_fig_2.png
docs/reference/figures/paper_fig_3.png
docs/reference/filter_bases.html
docs/reference/get_distribution.html
docs/reference/get_heteroplasmy.html
docs/reference/get_raw_counts_allele.html
docs/reference/get_wilcox_test.html
docs/reference/index.html
docs/reference/plot_allele_frequency.html
docs/reference/plot_base_coverage.html
docs/reference/plot_batch.html
docs/reference/plot_cells_coverage.html
docs/reference/plot_condition.html
docs/reference/plot_coordinate_cluster.html
docs/reference/plot_coordinate_heteroplasmy.html
docs/reference/plot_correlation_bases.html
docs/reference/plot_distance_matrix.html
docs/reference/plot_distribution.html
docs/reference/plot_dpt.html
docs/reference/plot_genome_coverage.html
docs/reference/plot_heatmap.html
docs/reference/plot_heteroplasmy.html
docs/reference/plot_heteroplasmy_variability.html
docs/reference/plot_spider_chart.html
docs/reference/vi_comparison.html
docs/sitemap.xml
inst/.DS_Store
inst/extdata/.DS_Store
inst/extdata/CD34_colonies_table.txt
inst/extdata/Mus_musculus.GRCm38.dna.chromosome.MT.fa
inst/extdata/after_qc.Rda
inst/extdata/bg.fasta.txt
inst/extdata/coordinate_dm.Rda
inst/extdata/hb.fasta.txt
inst/extdata/meta_data_ana_final_big.Rda
inst/extdata/meta_data_ana_final_small.Rda
inst/extdata/meta_data_antonio_final.Rda
inst/extdata/mt_start_end.txt
inst/extdata/name_cells_fig_2.Rda
inst/extdata/name_cells_fig_2_analysis.Rda
inst/extdata/name_cells_fig_5_all.Rda
inst/extdata/name_cells_fig_5_all_analysis.Rda
inst/extdata/output_SNP_ana_mt.Rda
inst/extdata/output_SNP_antonio_mt.Rda
inst/extdata/output_SNP_mt.Rda
inst/extdata/output_SNP_mt_fig_2_new.Rda
inst/extdata/output_SNP_mt_fig_5_new.Rda
man/.DS_Store
man/choose_features_clustering.Rd man/clustering_angular_distance.Rd man/detect_insertion.Rd man/dpt_test.Rd
man/figures/paper_fig_1.png
man/figures/paper_fig_2.png
man/figures/paper_fig_3.png
man/filter_bases.Rd man/get_distribution.Rd man/get_heteroplasmy.Rd man/get_raw_counts_allele.Rd man/get_wilcox_test.Rd man/plot_allele_frequency.Rd man/plot_base_coverage.Rd man/plot_batch.Rd man/plot_cells_coverage.Rd man/plot_condition.Rd man/plot_coordinate_cluster.Rd man/plot_coordinate_heteroplasmy.Rd man/plot_correlation_bases.Rd man/plot_distance_matrix.Rd man/plot_distribution.Rd man/plot_dpt.Rd man/plot_genome_coverage.Rd man/plot_heatmap.Rd man/plot_heteroplasmy.Rd man/plot_heteroplasmy_variability.Rd man/plot_spider_chart.Rd man/vi_comparison.Rd
tests/.DS_Store
tests/testthat.R tests/testthat/test_clustering_angular_distance.R tests/testthat/test_get_heteroplasmy.R
vignettes/.DS_Store
vignettes/.Rhistory
vignettes/.gitignore
vignettes/Ludwig_et_al_example_notebook.Rmd vignettes/cell_competition_bulk_data_mt_example_notebook.Rmd vignettes/cell_competition_mt_example_notebook.Rmd vignettes/lineage_tracing_example_notebook.Rmd
ScialdoneLab/MitoHEAR documentation built on June 11, 2022, 7:18 a.m.