API for HCGB-IGTP/HCGB.IGTP.DAnalysis
Useful in-house functions for multiple analysis
| Global functions | |
|---|---|
| %!in% | Man page |
| DESeq2_HCGB_function | Man page Source code |
| FGSEA_GSEA | Man page Source code |
| FGSEA_GSEA_loop | Man page Source code |
| GR_list_samples | Man page Source code |
| GRanges_subsetter | Man page Source code |
| adjust_samples | Man page Source code |
| analysis_DESeq | Man page Source code |
| beta_values_plots | Man page Source code |
| check.background | Source code |
| check.mean_intensity | Source code |
| check.na_probes | Source code |
| check_covariates | Man page Source code |
| check_rank_design | Man page Source code |
| check_reduced_LRT | Man page Source code |
| check_terms_matrix | Man page Source code |
| colnames_GRanges | Man page Source code |
| convertDate | Man page Source code |
| create_col_palette | Man page Source code |
| create_col_palette2 | Source code |
| create_matrix_overlaps | Man page Source code |
| create_matrix_overlaps_by_seqnames | Man page Source code |
| create_overlaps | Man page Source code |
| create_rank_plots | Source code |
| create_report | Man page Source code |
| create_upset | Man page Source code |
| create_upset_data | Man page Source code |
| create_upset_plot | Man page Source code |
| custom_annotation | Man page Source code |
| delete_na | Man page Source code |
| df.factorizer | Man page Source code |
| dim_GRanges | Man page Source code |
| discard_0_counts | Man page Source code |
| discard_lowCounts | Man page Source code |
| discard_lowCounts_df | Man page Source code |
| dreduction_function | Man page Source code |
| enricher_loop | Man page |
| exploratory_plots | Man page Source code |
| filter_bump_table | Man page Source code |
| filter_dmpFinder_table | Man page Source code |
| filter_signficant_DESEQ | Man page Source code |
| filter_signficant_limma | Man page Source code |
| getDataF_sesameQC_calcStats | Source code |
| get_GSEA_datasets | Man page Source code |
| get_Results_DDS | Man page Source code |
| get_all_data_DESeq2 | Man page Source code |
| get_beta_mean_vals | Man page Source code |
| get_chr_len | Man page Source code |
| get_cols | Man page Source code |
| get_comparison_resultsNames | Man page Source code |
| get_data_upset | Man page Source code |
| get_dim | Source code |
| get_dim.filt | Man page Source code |
| get_freq | Man page Source code |
| get_gene_annotation | Man page Source code |
| get_gene_coordinates | Man page Source code |
| get_keys.qcs | Source code |
| get_length_vect | Man page Source code |
| get_limma_results | Man page Source code |
| get_pfb | Man page Source code |
| get_probes_limma | Man page Source code |
| get_rows | Man page Source code |
| get_single_UpSet_plot | Man page Source code |
| get_topGO_data | Man page Source code |
| get_vect | Man page Source code |
| ggboxplot_scatter | Man page Source code |
| ggscatter_plotRegression | Man page Source code |
| gprofiler_analysis | Man page Source code |
| limma_DE_function | Man page Source code |
| litfover_func | Man page Source code |
| load_RnBeads_object | Man page Source code |
| load_beta_values | Man page Source code |
| loader | Man page Source code |
| locus_plotter | Man page Source code |
| maplot | Man page |
| my_volcanoplot_region | Man page |
| my_volcanoplot_sites | Man page |
| pheatmap_log | Man page Source code |
| plot.grid.ggscatterBoxplot | Man page Source code |
| plot.grid.ggscatterRegression | Man page Source code |
| plotCN.here | Man page |
| plotCN_zoom | Man page Source code |
| plot_DESeq2_pvalues | Man page Source code |
| plot_GSEA | Man page Source code |
| plot_batch_effect | Man page Source code |
| plot_control_means | Man page Source code |
| plot_gene_values | Man page Source code |
| plot_genes | Man page Source code |
| plot_identity.bar | Source code |
| plot_identity.bar_old | Source code |
| plot_representation | Man page Source code |
| print_plot_control_means | Man page Source code |
| produce_norm_plots | Man page Source code |
| rank_list_by | Man page Source code |
| read_genoCN | Man page Source code |
| read_pennCNV | Man page Source code |
| relevel_function | Man page Source code |
| sample_sheet_splitter | Source code |
| save_RnBeads_object | Man page Source code |
| save_bed_info | Man page Source code |
| save_jpeg | Man page Source code |
| save_norm_plots | Man page Source code |
| save_pdf | Man page Source code |
| save_plots_multiformat | Man page |
| save_png | Man page Source code |
| save_qc_plots | Man page Source code |
| sessionInfo_write | Man page Source code |
| vector_splitter | Man page Source code |
| volcanoplot | Man page |
| wgcna_blockwiseModules | Source code |
| wgcna_dynamicModules | Source code |
| wgcna_eigengenes_module | Source code |
| wgcna_labeledHeatmap | Source code |
| wgcna_soft_thresh | Source code |
| write_norm_files | Man page Source code |
| write_qc_files | Man page Source code |
