Files in NathanSkene/EWCE
Expression Weighted Celltype Enrichment

.Rbuildignore
.github/.gitignore
.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md
.github/workflows/check-bioc-docker.yml
.gitignore
DESCRIPTION
Dockerfile
NAMESPACE
NEWS.md R/add_res_to_merging_list.r R/assign_cores.r R/bin_columns_into_quantiles.r R/bin_specificity_into_quantiles.r R/bootstrap_enrichment_test.R R/bootstrap_plot.R R/calc_quantiles.R R/calculate_meanexp_for_level.R R/calculate_specificity_for_level.R R/cell_list_dist.r R/check_annotLevels.R R/check_args_for_bootstrap_plot_generation.R R/check_bootstrap_args.R R/check_controlled_args.R R/check_ewce_expression_data_args.R R/check_ewce_genelist_input.r R/check_full_results.R R/check_generate_controlled_bootstrapped_geneset.R R/check_group_name.R R/check_nas.R R/check_numeric.R R/check_percent_hits.R R/check_sce.R R/check_species.R R/controlled_geneset_enrichment.r R/convert_new_ewce_to_old.r R/convert_old_ewce_to_new.r R/create_background_multilist.R R/create_list_network.R R/create_quadrants.R R/ctd_to_sce.R R/delayedarray_normalize.R R/drop_nonexpressed_cells.R R/drop_nonexpressed_genes.R R/drop_uninformative_genes.r R/dt_to_df.R R/ewce_expression_data.r R/ewce_plot.r R/example_bootstrap_results.R R/example_transcriptome_results.R R/extract_matrix.R R/filter_ctd_genes.R R/filter_genes_without_1to1_homolog.r R/filter_nonorthologs.R R/filter_variance_quantiles.r R/fix_bad_hgnc_symbols.r R/fix_bad_mgi_symbols.r R/fix_celltype_names.R R/fix_celltype_names_full_results.R R/generate_bootstrap_plots.r R/generate_bootstrap_plots_for_transcriptome.r R/generate_celltype_data.r R/generate_controlled_bootstrap_geneset.r R/get_celltype_table.r R/get_ctd_levels.R R/get_ctd_matrix_names.R R/get_exp_data_for_bootstrapped_genes.R R/get_graph_theme.R R/get_sig_results.R R/get_summed_proportions.r R/is_32bit.R R/is_celltypedataset.R R/is_ctd_standardised.R R/is_delayed_array.R R/is_matrix.R R/is_sparse_matrix.R R/list_species.R R/load_rdata.R R/max_ctd_depth.R R/merge_ctd.R R/merge_sce.R R/merge_sce_list.R R/merge_two_expfiles.r R/merged_ewce.r R/message_parallel.R R/messager.R R/myScalesComma.R R/package.R R/plot_bootstrap_plots.R R/plot_ctd.R R/plot_log_bootstrap_distributions.R R/plot_with_bootstrap_distributions.R R/prep_dendro.r R/prepare_genesize_control_network.r R/prepare_tt.R R/rNorm.R R/read_ctd.R R/report_dge.R R/report_results.R R/run_deseq2.R R/run_limma.r R/run_mast.r R/sce_lists_apply.R R/sce_merged_apply.R R/sct_normalize.R R/standardise_ctd.R R/to_dataframe.R R/to_delayed_array.R R/to_sparse_matrix.R R/zeisel2018_functions.r README.Rmd README.md
inst/CITATION
inst/cit/EWCE.bib
inst/cit/nature.csl
inst/extdata/bootstrap_results.rda
inst/extdata/tt_results.rda
inst/hex/cell2.png
inst/hex/gene1.png
inst/hex/hex.png
inst/hex/hexSticker.Rmd man/EWCE-package.Rd man/add_res_to_merging_list.Rd man/assign_cores.Rd man/bin_columns_into_quantiles.Rd man/bin_specificity_into_quantiles.Rd man/bootstrap_enrichment_test.Rd man/bootstrap_plot.Rd man/calc_quantiles.Rd man/calculate_meanexp_for_level.Rd man/calculate_specificity_for_level.Rd man/cell_list_dist.Rd man/check_annotLevels.Rd man/check_args_for_bootstrap_plot_generation.Rd man/check_bootstrap_args.Rd man/check_controlled_args.Rd man/check_ewce_expression_data_args.Rd man/check_ewce_genelist_inputs.Rd man/check_full_results.Rd man/check_generate_controlled_bootstrap_geneset.Rd man/check_group_name.Rd man/check_nas.Rd man/check_numeric.Rd man/check_percent_hits.Rd man/check_sce.Rd man/check_species.Rd man/controlled_geneset_enrichment.Rd man/convert_new_ewce_to_old.Rd man/convert_old_ewce_to_new.Rd man/create_background_multilist.Rd man/create_list_network.Rd man/ctd_to_sce.Rd man/delayedarray_normalize.Rd man/drop_nonexpressed_cells.Rd man/drop_nonexpressed_genes.Rd man/drop_uninformative_genes.Rd man/dt_to_df.Rd man/ewce_expression_data.Rd man/ewce_plot.Rd man/example_bootstrap_results.Rd man/example_transcriptome_results.Rd man/extract_matrix.Rd man/filter_ctd_genes.Rd man/filter_genes_without_1to1_homolog.Rd man/filter_nonorthologs.Rd man/filter_variance_quantiles.Rd man/fix_bad_hgnc_symbols.Rd man/fix_bad_mgi_symbols.Rd man/fix_celltype_names.Rd man/fix_celltype_names_full_results.Rd man/generate_bootstrap_plots.Rd man/generate_bootstrap_plots_for_transcriptome.Rd man/generate_celltype_data.Rd man/generate_controlled_bootstrap_geneset.Rd man/get_celltype_table.Rd man/get_ctd_levels.Rd man/get_ctd_matrix_names.Rd man/get_exp_data_for_bootstrapped_genes.Rd man/get_graph_theme.Rd man/get_sig_results.Rd man/get_summed_proportions.Rd man/is_32bit.Rd man/is_celltypedataset.Rd man/is_ctd_standardised.Rd man/is_delayed_array.Rd man/is_matrix.Rd man/is_sparse_matrix.Rd man/list_species.Rd man/load_rdata.Rd man/max_ctd_depth.Rd man/merge_ctd.Rd man/merge_sce.Rd man/merge_sce_list.Rd man/merge_two_expfiles.Rd man/merged_ewce.Rd man/message_parallel.Rd man/messager.Rd man/myScalesComma.Rd man/plot_bootstrap_plots.Rd man/plot_ctd.Rd man/plot_log_bootstrap_distributions.Rd man/plot_with_bootstrap_distributions.Rd man/prep.dendro.Rd man/prep_dendro.Rd man/prepare_genesize_control_network.Rd man/prepare_tt.Rd man/report_dge.Rd man/report_results.Rd man/run_deseq2.Rd man/run_limma.Rd man/run_mast.Rd man/sce_lists_apply.Rd man/sce_merged_apply.Rd man/sct_normalize.Rd man/standardise_ctd.Rd man/to_dataframe.Rd man/to_delayed_array.Rd man/to_sparse_matrix.Rd tests/testthat.R tests/testthat/test-CTD_mean.R tests/testthat/test-CTD_specificity.R tests/testthat/test-DelayedArray.R tests/testthat/test-bin_columns_into_quantiles.r tests/testthat/test-bootstrap_enrichment_test.R tests/testthat/test-bootstrap_enrichment_test_2.R tests/testthat/test-celltype_specificity_Aif1_Pvalb.R tests/testthat/test-check_percent_hits.R tests/testthat/test-controlled_geneset_enrichment.R tests/testthat/test-ewce_expression_data.R tests/testthat/test-filter_ctd_genes.R tests/testthat/test-filter_genes_without_1to1_homolog.R tests/testthat/test-fix_bad_mgi_symbols.r tests/testthat/test-generate_celltype_data.r tests/testthat/test-get_celltype_table.r tests/testthat/test-list_species.R tests/testthat/test-merge_ctd.R tests/testthat/test-merge_two_expfiles.R tests/testthat/test-run_DGE.R vignettes/EWCE.Rmd vignettes/extended.Rmd
NathanSkene/EWCE documentation built on Aug. 6, 2022, 9:27 a.m.