Files in HCGB-IGTP/HCGB.IGTP.DAnalysis

Useful in-house functions for multiple analysis

R/DESeq2_functions.R R/DE_functions.R R/EPIC_functions.R R/EPICv2_functions.R R/GDAcyto_functions.R R/GRanges_functions.R R/RnBeads_functions.R R/UpSetR_functions.R R/WGCNA_functions.R R/functional_functions.R R/functions.R R/limma_functions.R R/meffil_functions.R R/plotting_functions.R R/toAdd.R README.md code_example/README.md code_example/example_UpsetR.md code_example/example_WGCNA.md code_example/parallel_code.R dev/check_package.R dev/create_R_package.R dev/install_package.R dev/update_R_package.R man/DESeq2_HCGB_function.Rd man/FGSEA_GSEA.Rd man/FGSEA_GSEA_loop.Rd man/GR_list_samples.Rd man/GRanges_subsetter.Rd man/adjust_samples.Rd man/analysis_DESeq.Rd man/beta_values_plots.Rd man/check_covariates.Rd man/check_rank_design.Rd man/check_reduced_LRT.Rd man/check_terms_matrix.Rd man/colnames_GRanges.Rd man/convertDate.Rd man/create_col_palette.Rd man/create_matrix_overlaps.Rd man/create_matrix_overlaps_by_seqnames.Rd man/create_overlaps.Rd man/create_report.Rd man/create_upset.Rd man/create_upset_data.Rd man/create_upset_plot.Rd man/custom_annotation.Rd man/delete_na.Rd man/df.factorizer.Rd man/dim_GRanges.Rd man/discard_0_counts.Rd man/discard_lowCounts.Rd man/discard_lowCounts_df.Rd man/dreduction_function.Rd man/enricher_loop.Rd man/exploratory_plots.Rd man/filter_bump_table.Rd man/filter_dmpFinder_table.Rd man/filter_signficant_DESEQ.Rd man/filter_signficant_limma.Rd man/get_GSEA_datasets.Rd man/get_Results_DDS.Rd man/get_all_data_DESeq2.Rd man/get_beta_mean_vals.Rd man/get_chr_len.Rd man/get_cols.Rd man/get_comparison_resultsNames.Rd man/get_data_upset.Rd man/get_dim.filt.Rd man/get_freq.Rd man/get_gene_annotation.Rd man/get_gene_coordinates.Rd man/get_length_vect.Rd man/get_limma_results.Rd man/get_pfb.Rd man/get_probes_limma.Rd man/get_rows.Rd man/get_single_UpSet_plot.Rd man/get_topGO_data.Rd man/get_vect.Rd man/ggboxplot_scatter.Rd man/ggscatter_plotRegression.Rd man/gprofiler_analysis.Rd man/grapes-not-in-grapes.Rd man/limma_DE_function.Rd man/litfover_func.Rd man/load_RnBeads_object.Rd man/load_beta_values.Rd man/loader.Rd man/locus_plotter.Rd man/maplot.Rd man/my_volcanoplot_region.Rd man/my_volcanoplot_sites.Rd man/pheatmap_log.Rd man/plot.grid.ggscatterBoxplot.Rd man/plot.grid.ggscatterRegression.Rd man/plotCN.here.Rd man/plotCN_zoom.Rd man/plot_DESeq2_pvalues.Rd man/plot_GSEA.Rd man/plot_batch_effect.Rd man/plot_control_means.Rd man/plot_gene_values.Rd man/plot_genes.Rd man/plot_representation.Rd man/print_plot_control_means.Rd man/produce_norm_plots.Rd man/rank_list_by.Rd man/read_genoCN.Rd man/read_pennCNV.Rd man/relevel_function.Rd man/save_RnBeads_object.Rd man/save_bed_info.Rd man/save_jpeg.Rd man/save_norm_plots.Rd man/save_pdf.Rd man/save_plots_multiformat.Rd man/save_png.Rd man/save_qc_plots.Rd man/sessionInfo_write.Rd man/vector_splitter.Rd man/volcanoplot.Rd man/write_norm_files.Rd man/write_qc_files.Rd other_code/BUSCO_plots.R other_code/example_MEAL.R other_code/expression_methylation-regression.R other_code/regression_plots.R