Man pages for cparsania/FungiExpresZ
FungiExpresZ: Fungal gene expression data analysis and visualizations
| app_server | app server |
| app_ui | app_ui |
| badge_custom_url | get custom badge url |
| badge_devel_url | get github repo version devel bedge |
| badge_github_release_url | create a custom badge url for github release |
| check_var_types | validate vars |
| cross_ref_go_db | Cross reference GO_ID to GID mapping from GO.db data |
| decorate_ggplot | Decorate GG plot |
| dot-filter_samples_by_mapping_rate | Filter FPKM matrix by mapping rate |
| dot-get_annotations_from_fungal_sra_run_info_table | Prepare SRA sample annotations from fungal_sra_run_info_table |
| dot-get_annotations_from_sradb | Prepare SRA sample annotations from SRAdb |
| generate_random_strings | Generates n random string of length 10 |
| get_ca_gene_names_mapping | Map Candida albicans genes between orf_XXXXX and C1_XXXXX |
| get_density | get_density |
| get_expression_mats_dir_path | Get absolute path for the expression matrix .rds files. It... |
| get_gg_colors | Get character vector of ggplot colors in default order |
| get_test_data | get random sample of gene expression matrix |
| get_updated_existing_annotations | Get updated annotations objects (sample_info &... |
| lm_eqn | lm_eqn |
| mod_add_gene_groups | add_gene_groups_ui and add_gene_groups |
| mod_add_sample_group | add_sample_group_ui and add_sample_group |
| mod_cluster_wise_sample_information | cluster_wise_sample_information_ui and... |
| mod_display_active_groups | display_active_groups_ui and display_active_groups_server |
| mod_display_sra_sample_info | display_sra_sample_info_ui and display_sra_sample_info_server |
| mod_download_gene_expression_matrix | mod_download_gene_expression_matrix_ui and... |
| mod_download_go_data | download_go_data_ui and download_go_data_server |
| mod_export_base_graphics | export_base_graphics_ui and export_base_graphics |
| mod_export_plot | export_plot_ui export_plot |
| mod_functional_analysis | functional_analysis_ui and functional_analysis_server |
| mod_gene_group_selection | gene_group_selection_ui and gene_group_selection |
| mod_ggplot_fill_and_facet | ggplot_fill_and_facet_ui and ggplot_fill_and_facet |
| mod_ggplot_fill_colour | ggplot_fill_colour_ui and ggplot_fill_colour |
| mod_joy_plot_fill_and_facet | joy_plot_fill_and_facet_ui and joyplot_fill_and_facet |
| mod_pathway_analysis | mod_pathway_analysis_ui and mod_pathway_analysis_server |
| mod_plot_title_and_axis_label | plot_title_and_axis_label_ui and... |
| mod_word_cloud | word_cloud_ui and word_cloud_server |
| my_filter | create column filters |
| perform_go_enrichmet | Perform GO enrichment using clusterProfiler |
| prepare_annotations_for_fungiexpres_data_matrix | Prepare SRA sample annotations required for FungiExpresZ. |
| prepare_fungiexpresz_fpkm_matrix_rds_files_from_stringTie_output | Prepare FPKM matrix from stringTie output |
| reorder_clusters | reorder_clusters |
| run_app | Run the Shiny Application |
| shinyInput | create shiny inputs |
| text_to_clean_document | Convert text into clean document using several functions from... |
| text_to_tibble | Given a string separated by specified deliminator, the... |
| tibble_to_row_clusters | Given a tibble of gene expression matrix, perform row wise... |
| tibble_to_rowwise_sd_zs | given the tibble and column indices add columns of row wise... |
