Man pages for espors/idepGolem
Integrated Differential Expression and Pathway Analysis
| add_legend | Add a legend |
| background_pathway_sets | Background gene pathway sets |
| basic_heatmap | Heatmap of the data |
| basic_heat_sub | Heatmap of User brush selection |
| bicluster_summary_message | Summary of biclust |
| build_pathway_query | Create SQL query statement for reading pathway db |
| change_names | Change comparison names |
| check_object_state | Check object state |
| chr_counts_ggplot | Creates a barplot of the count data by chr |
| chr_normalized_ggplot | Creates a barplot of the normalized data by chr |
| chromosome_plotly | Plotly of chromosome position |
| clean_gene_set | Data cleaning on gene sets |
| clean_query | Clean gene query |
| cluster_heat_click_info | Interactive click text for subheatmap |
| colorpanel2 | Pathview function... |
| connect_convert_db | Connect to the convertIDs database and return the objects. |
| connect_convert_db_org | Connect to the convertIDs database for the species and return... |
| conversion_counts_message | Data processing message |
| convert_data | Convert expression data rownames to ensembl |
| convert_ensembl_to_entrez | Convert IDs from ensembl to entrez |
| convert_id | Convert gene IDs to ensembl data. |
| cor_plot | Create a correlation plot from heatmap data |
| counts_bias_message | Create message for sequencing depth bias |
| data_frame_with_list | GET RID OF LISTS IN A DATA FRAME |
| deg_click_info | HTML code for sub-heatmap selected cell |
| deg_deseq2 | Differential expression using DESeq2 package |
| deg_heat_data | Find data for the heatmap |
| deg_heatmap | Heatmap for significant contrast genes |
| deg_heat_sub | Plot brush selection from main heatmap |
| deg_information | returns results from DEG analysis |
| deg_limma | Differential expression using limma package |
| detect_groups | Detect groups by sample names |
| dist_functions | List of distance functions for hierarchical clustering |
| doc_hist | Density plot for the processed data |
| draw_sample_tree | Draw a dendogram of data samples |
| dynamic_range | Dynamic Range |
| eda_boxplot | Boxplot for processed data |
| eda_density | Density plot for the processed data |
| eda_scatter | Scatterplot for EDA on processed data |
| enrich_barplot | Generate barplot for enrichment results |
| enrichment_network | ENRICHMENT NETWORK FUNCTION |
| enrichment_tree_plot | Dendogram of enriched pathways |
| enrich_net | numChar=100 maximum number of characters n=200 maximum number... |
| experiment_design_txt | Create a string of the model design |
| extract_fcfdr | Extract fold change and FDR for each comparison from limma |
| extract_under | Replace underscore Find any instances of "_" and replace them... |
| extract_word | Extract a word |
| fct_01_load_data.R | fct_01_load_data.R This file holds all of the main data... |
| fct_02_pre_process.R | fct_02_pre_process.R This file holds all of the main data... |
| fct_03_heatmap.R | fct_03_heatmap.R This file holds all of the main data... |
| fct_05_pca.R | fct_05_pca.R This file holds all of the main data analysis... |
| fct_06_deg1.R | fct_06_deg1.R This file holds all of the main data analysis... |
| fct_06_pathway.R | fct_06_pathway.R This file holds all of the main data... |
| fct_07_genome.R | fct_07_genome.R This file holds all of the main data analysis... |
| fct_08_bicluster.R | fct_08_bicluster.R This file holds all of the main data... |
| fct_analysis_random.R | fct_analysis_random.R Miscellaneous data analysis functions... |
| fct_database.R | fct_database.R: A fie with all functions to deal with... |
| fgsea_data | Pathway analysis with the FGSEA package |
| find_contrast_samples | Determine samples in selected contrast |
| find_id_type_by_id | Find the ID type |
| find_overlap | Find overlap for pathway analysis |
| find_overlap_gmt | Calculate overlap for species with GMT file |
| find_species_by_id | Find a species by ID |
| find_species_by_id_name | Find a species by ID |
| find_species_id_by_ensembl | Find a species id by ensembl dataset name |
| gage_data | Pathway analysis with gage package |
| gene_counts_ggplot | Creates a barplot of the count of genes by type |
| gene_info | Retrieve detailed info on genes |
| generate_colors | Generate colors for plots, solving the problem of not having... |
| generate_descr | Write paragraph containing process details |
| genes_stat_table | Create a table from DEG results |
| get_all_gene_names | Get all matched gene names |
| get_biclustering | Get bicuster information |
| get_biclust_table_data | Table of biclustering data |
| get_gene_info | Retrieve detailed gene information |
| get_gsva_plot_data | Data from GSVA plot |
| get_idep_data | Load iDEP data |
| get_module_plot | Dendogram plot of WGCNA modules |
| get_network | Network of top genes |
| get_network_plot | Network of top genes, plot |
| get_pathway_list_data | Create pathway table with gene sets |
| get_pc | Prepare PC data |
| get_pc_variance | Get variance percentages |
| get_pgsea_plot_all_samples_data | Data from PGSEA plot all samples |
| get_pgsea_plot_data | Data from PGSEA plot |
| get_plot_height | Gets plot height size from session$clientdata |
| get_plot_width | Gets plot width dimensions from session$clientdata |
| get_wgcna | Utilize WGCNA function |
| get_wgcna_modules | List WGCNA modules |
| gg_color_hue | 'ggplot' colors |
| gmt_category | Database choices for the converted IDs |
| gsva_data | Pathway analysis with the GSVA package |
| hcluster_functions | List of method functions for hierarchical clustering |
| heat_click_info | HTML code for sub-heatmap selected cell |
| heatmap_main | Draw a heatmap of processed data |
| heat_sub | Draw sub heatmap from brush input |
| hyperText | Convert regular text to hypertext with links |
| individual_plots | Individual plotting function for genes |
| input_data | Load basic data information |
| kegg_pathway | Use KEGG to create a pathway diagram |
| k_means_elbow | Draw an elbow plot for k-cluster selection |
| limma_value | DEG analysis function |
| list_block_factors_ui | Get the block factor choices |
| list_comp_venn | List comparisons for venn diagram plot |
| list_factors_ui | Create choices and title for model factors |
| list_interaction_terms_ui | List model interaction terms |
| list_model_comparisons_ui | Create model comparisons choices |
| loose_rock_proper | Capitalizes the first letter in all words of a string |
| make_pull_down_menu | Create a pull down menu |
| max_fun | Calculate max of vector |
| MDS_plot | MDS plot |
| mean_fun | Calculate mean of vector |
| mean_sd_plot | Mean vs. Standard Deviation plot |
| median_fun | Calculate median of vector |
| merge_data | Merge data from gene info and processed data |
| mod_label_server | Server component to customize gene labels |
| mod_label_ui | UI component to customize gene labels |
| network_data | VisNetwork data |
| network_enrich_data | Gene vector query for enrichment |
| pathview.stamp | PATHVIEW SOURCE FUNCTION |
| pathway_select_data | Get data from genes in selected pathway |
| pathway_source_info | retrieve source info for pathway db |
| PCA_biplot | Principal Component Analysis with PCAtools package |
| PCA_plot | Principal component analysis plot |
| PCA_plot_3d | Principal component analysis 3D plot |
| PCA_Scree | Principal Component Analysis with PCAtools package |
| PCAtools_eigencorplot | Principal Component Analysis with PCAtools package |
| pc_factor_correlation | Correlations Between Principle Components and Factors |
| pgsea_data | Pathway analysis with the PGSEA package |
| pgsea_plot_all | Pathway analysis with the PGSEA package on all samples |
| plot_deg_scatter | Scatter plot of the comparison groups |
| plot_gsva | Heatmap of GSVA pathway analysis |
| plot_ma | Plot mean expression and fold change |
| plot_mean_connectivity | Mean connectivity plot |
| plot_pgsea | Heatmap of PGSEA pathway analysis |
| plot_scale_independence | Scale independence plot |
| plot_upset | Plot upset graph |
| plot_venn | Create a venn diagram plot |
| plot_volcano | Volcano DEG plot |
| prepare_module_csv | prepare_module_csv |
| prepare_module_csv_filter | prepare_module_csv_filter |
| prep_download | Prep heatmap data for download |
| pre_process | Pre-Process the data |
| prep_venn | Prep data for venn diagram |
| print_dataframe | Print out a matrix's content as R code to regenerate the... |
| print_vector | print the content of a vector as R code for the reconstruc of... |
| process_heatmap_data | Heatmap data processing |
| proper | Capitalize first letter |
| reactome_data | Pathway analysis with reactome package |
| read_gene_sets | Read pathway gene sets |
| read_gmt | Read .gmt file |
| read_gmt_robust | Read gene sets GMT file This functions cleans and converts... |
| read_pathway_sets | Read pathway sets for gene query |
| refine_ggplot2 | Change ggplot2 plots |
| remove_pathway_id | Remove Pathway ID from pathway name Only for GO and KEGG... |
| remove_pathway_id_second | Remove Pathway ID from pathway name in PGSEA Only for GO and... |
| render.kegg.node | PATHVIEW SOURCE FUNCTION... |
| rowname_id_swap | Swap rowname IDs for data matrix |
| rRNA_counts_ggplot | Creates a barplot of the count data by gene type |
| run_app | Run the Shiny Application |
| sd_density | Density plot of data standard deviation |
| select_reference_levels_ui | Refernce levels for selected factor |
| showGeneIDs | Show sample gene IDs in modal |
| sig_genes_plot | Significant genes bar plot |
| sub_heat_ann | Create annotation for shiny subheatmap |
| sum_fun | Calculate sum of vector |
| total_counts_ggplot | Creates a barplot of the count data |
| transform_comparisons | comparisons in all levels of the other factor "stage: MN vs.... |
| t_SNE_plot | t-SNE plot |
| utils_analysis_random.R | utils_analysis_random.R Miscellaneous helper functions here,... |
| utils_ui.R | utils_ui.R These are helper functions for ui code, shiny code... |
| vis_network_plot | VisNetwork plot |
| volcano_data | Data processing for volcano and ma plot |
| wrap_strings | Wrapping long text by adding a new line character |
