Files in NathanSkene/EWCE
Expression Weighted Celltype Enrichment

.Rbuildignore

.github/.DS_Store

.github/.gitignore

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md

.github/workflows/rworkflows.yml

.gitignore

DESCRIPTION

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/bootstrap_plots_for_transcriptome.R R/calculate_meanexp_for_level.R R/calculate_specificity_for_level.R R/cell_list_dist.r R/cells_in_ctd.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_mtc_method.R R/check_nas.R R/check_numeric.R R/check_percent_hits.R R/check_sce.R R/check_species.R R/compute_gene_counts.R R/compute_gene_scores.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_exp_mats.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_sig_results.R R/get_summed_proportions.r R/get_summed_proportions_iterate.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_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/theme_graph.R R/to_dataframe.R R/to_delayed_array.R R/to_sparse_matrix.R R/zeisel2018_functions.r README.Rmd README.md

inst/.DS_Store

inst/CITATION

inst/cit/EWCE.bib

inst/cit/nature.csl

inst/extdata/bootstrap_results.rda

inst/extdata/tt_results.rda

inst/hex/2BIgqrmzc0GSaaAGOqSeAu.jpg

inst/hex/hex.png

NathanSkene/EWCE documentation built on Nov. 3, 2024, 8:16 a.m.

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NathanSkene/EWCE
Expression Weighted Celltype Enrichment

Files in NathanSkene/EWCE
Expression Weighted Celltype Enrichment

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NathanSkene/EWCE Expression Weighted Celltype Enrichment

Files in NathanSkene/EWCE Expression Weighted Celltype Enrichment

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NathanSkene/EWCE
Expression Weighted Celltype Enrichment

Files in NathanSkene/EWCE
Expression Weighted Celltype Enrichment