Files in rdocking/amlpmpsupport
Support Functions for AML PMP RNA-Seq Stratification Manuscript
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml.bak
.github/workflows/check_and_document.yaml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/clustering_helpers.r
R/cna_workflow.r
R/dataframe_builders.r
R/db_helpers.r
R/ifxparsers.r
R/plotting_functions.r
R/random_forest_helpers.r
R/run_gage_for_feature.r
R/run_voom_for_feature.r
R/snv_indel_helpers.r
R/stratification_functions.r
R/subset_genes_for_plots.r
R/survival_functions.r
R/utility_functions.r
R/utils-pipe.R
README.md
_pkgdown.yml
amlpmpsupport.Rproj
codecov.yml
docs/404.html
docs/LICENSE-text.html
docs/articles/amlpmpsupport-examples.html
docs/articles/index.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/add_colour_vector_to_concordance.html
docs/reference/add_entrez_ids_from_hugo_genes.html
docs/reference/apply_eln2015_cyto.html
docs/reference/apply_eln2017_cyto.html
docs/reference/apply_eln2017_rna.html
docs/reference/apply_expression_signature_reclassification.html
docs/reference/aps_volcano_plot-1.png
docs/reference/aps_volcano_plot.html
docs/reference/calculate_reference_set_coefficient_of_variation.html
docs/reference/calculate_reference_set_mean_expression.html
docs/reference/connect_to_aml_project_orm.html
docs/reference/construct_rna_qc_dataframe.html
docs/reference/construct_sailfish_gene_dataframe.html
docs/reference/convert_sailfish_df_to_matrix.html
docs/reference/density_plotter-1.png
docs/reference/density_plotter.html
docs/reference/downregulated_genes.html
docs/reference/eng_log_breaks.html
docs/reference/expression_matrix_to_long_df.html
docs/reference/figures/lifecycle-archived.svg
docs/reference/figures/lifecycle-defunct.svg
docs/reference/figures/lifecycle-deprecated.svg
docs/reference/figures/lifecycle-experimental.svg
docs/reference/figures/lifecycle-maturing.svg
docs/reference/figures/lifecycle-questioning.svg
docs/reference/figures/lifecycle-soft-deprecated.svg
docs/reference/figures/lifecycle-stable.svg
docs/reference/figures/lifecycle-superseded.svg
docs/reference/fit_coxph.html
docs/reference/gather_expression_matrix_to_tidy_df.html
docs/reference/get_cluster_assignments_for_k.html
docs/reference/ggsave_pdf_and_png.html
docs/reference/grid_arrange_shared_legend.html
docs/reference/group_tally_table.html
docs/reference/hit_plotter-1.png
docs/reference/hit_plotter.html
docs/reference/index.html
docs/reference/limma_logFC_to_signed_foldchange.html
docs/reference/log2_plus1_transform.html
docs/reference/long_df_to_ranked_matrix.html
docs/reference/matrix_glimpse.html
docs/reference/munge_voom_to_ipa.html
docs/reference/nest_libraries_by_patient.html
docs/reference/num_to_text.html
docs/reference/parse_pavfinder_0.2.0.html
docs/reference/parse_pavfinder_0.3.0.html
docs/reference/pathway_enrichment_plot.html
docs/reference/pipe.html
docs/reference/plot_heatmap_for_k.html
docs/reference/plot_rf_predictions.html
docs/reference/plot_survival.html
docs/reference/plot_vars_by_coverage.html
docs/reference/plot_vars_by_vaf.html
docs/reference/pretty_kable.html
docs/reference/pretty_num.html
docs/reference/pull_enrichr_enriched_terms.html
docs/reference/pull_enrichr_terms_to_plot.html
docs/reference/random_forest_summary.html
docs/reference/read_filled_variant_tsv.html
docs/reference/rescale_genes_by_reference.html
docs/reference/retrieve_db_comments.html
docs/reference/retrieve_db_curated_results.html
docs/reference/retrieve_db_libraries.html
docs/reference/retrieve_db_paths.html
docs/reference/retrieve_db_specimens.html
docs/reference/rf_predictions.html
docs/reference/rna_seqc_parser.html
docs/reference/run_cna_workflow.html
docs/reference/run_gage_for_feature.html
docs/reference/run_voom_for_feature.html
docs/reference/sailfish_gene_parser_post_0.7.0.html
docs/reference/sailfish_isoform_parser_post_0.7.0.html
docs/reference/sailfish_isoform_parser_pre_0.7.0.html
docs/reference/scale_by_rolling_mean.html
docs/reference/select_by_position.html
docs/reference/split_gatk_format_vals.html
docs/reference/spread_expression_df_to_matrix.html
docs/reference/spread_filled_snv_df_to_wide.html
docs/reference/subset_genes_by_thresholds.html
docs/reference/subset_genes_for_plots.html
docs/reference/subset_heatmap.html
docs/reference/subset_pc_plot.html
docs/reference/subtype_to_disease.html
docs/reference/tfl_split_sort.html
docs/reference/train_caret_rf.html
docs/reference/upregulated_genes.html
docs/reference/volcano_plotter.html
man/add_colour_vector_to_concordance.Rd
man/apply_eln2015_cyto.Rd
man/apply_eln2017_cyto.Rd
man/apply_eln2017_rna.Rd
man/apply_expression_signature_reclassification.Rd
man/aps_volcano_plot.Rd
man/calculate_reference_set_coefficient_of_variation.Rd
man/calculate_reference_set_mean_expression.Rd
man/connect_to_aml_project_orm.Rd
man/construct_rna_qc_dataframe.Rd
man/construct_sailfish_gene_dataframe.Rd
man/convert_sailfish_df_to_matrix.Rd
man/density_plotter.Rd
man/downregulated_genes.Rd
man/eng_log_breaks.Rd
man/expression_matrix_to_long_df.Rd
man/expression_summary.Rd
man/figures/lifecycle-archived.svg
man/figures/lifecycle-defunct.svg
man/figures/lifecycle-deprecated.svg
man/figures/lifecycle-experimental.svg
man/figures/lifecycle-maturing.svg
man/figures/lifecycle-questioning.svg
man/figures/lifecycle-soft-deprecated.svg
man/figures/lifecycle-stable.svg
man/figures/lifecycle-superseded.svg
man/fit_coxph.Rd
man/gather_expression_matrix_to_tidy_df.Rd
man/get_cluster_assignments_for_k.Rd
man/ggsave_pdf_and_png.Rd
man/grid_arrange_shared_legend.Rd
man/group_tally_table.Rd
man/hit_plotter.Rd
man/limma_logFC_to_signed_foldchange.Rd
man/log2_plus1_transform.Rd
man/long_df_to_ranked_matrix.Rd
man/matrix_glimpse.Rd
man/munge_voom_to_ipa.Rd
man/nest_libraries_by_patient.Rd
man/num_to_text.Rd
man/parse_pavfinder_0.2.0.Rd
man/parse_pavfinder_0.3.0.Rd
man/pathway_enrichment_plot.Rd
man/pipe.Rd
man/plot_heatmap_for_k.Rd
man/plot_rf_predictions.Rd
man/plot_survival.Rd
man/plot_vars_by_coverage.Rd
man/plot_vars_by_vaf.Rd
man/pretty_kable.Rd
man/pretty_num.Rd
man/pull_enrichr_enriched_terms.Rd
man/pull_enrichr_terms_to_plot.Rd
man/random_forest_summary.Rd
man/read_filled_variant_tsv.Rd
man/rescale_genes_by_reference.Rd
man/retrieve_db_comments.Rd
man/retrieve_db_curated_results.Rd
man/retrieve_db_libraries.Rd
man/retrieve_db_paths.Rd
man/retrieve_db_specimens.Rd
man/rf_predictions.Rd
man/rna_seqc_parser.Rd
man/run_cna_workflow.Rd
man/run_gage_for_feature.Rd
man/run_voom_for_feature.Rd
man/sailfish_gene_parser_post_0.7.0.Rd
man/sailfish_isoform_parser_post_0.7.0.Rd
man/sailfish_isoform_parser_pre_0.7.0.Rd
man/scale_by_rolling_mean.Rd
man/select_by_position.Rd
man/split_gatk_format_vals.Rd
man/spread_expression_df_to_matrix.Rd
man/spread_filled_snv_df_to_wide.Rd
man/subset_genes_by_thresholds.Rd
man/subset_genes_for_plots.Rd
man/subset_heatmap.Rd
man/subset_pc_plot.Rd
man/subtype_to_disease.Rd
man/tfl_split_sort.Rd
man/train_caret_rf.Rd
man/upregulated_genes.Rd
man/volcano_plotter.Rd
tests/testthat.R
tests/testthat/test_plotting_functions.r
tests/testthat/test_stratification_functions.r
vignettes/amlpmpsupport-examples.Rmd
