Man pages for frhl/genoppi-v4
genoppi
| accession_gene_table | gene ID mapping table |
| add_genoppi_trace | add genoppi trace |
| add_hover_lines_volcano | add hover lines |
| add_layout_html_axes_scatterplot | layout for scatterplot |
| add_layout_html_axes_volcano | layout for volcano plot. |
| add_line_unity | add unity line |
| add_markers_search | search volcano plots |
| add_markers_search_pathway | search pathway plots |
| append_to_column | Append a string to a column |
| as.bait | as.bait |
| assign_freq | assign frequency |
| bold | bold |
| calc_fisher | Perform Fisher's exact test |
| calc_hyper | Perform hypergeometric test |
| calc_mod_ttest | Perform moderated t-test |
| catf | warnings to stderr |
| check_input | Check input data format |
| collapse_labels | collaps overlay data |
| color_distinct | distinct coloring |
| color_gradient | color gradient |
| draw_genoppi_venn | Draw venn diagrams |
| enumerate_replicate_combinations | enumerate replicate combinations |
| example_data | example proteomic data |
| genes_snps | SNP-to-gene mapping hash table |
| get_gene_lists | Read in gene lists |
| get_gwas_lists | Retreive GWAS catalog data for a given list of traits |
| get_inweb_list | Retrieve InWeb data for a given bait |
| get_pathways | Retreive pathway annotations for a list of genes |
| get_snp_lists | Map SNP lists to genes |
| gnomad_table | gnomAD table |
| goa_bp_table | GOA biological process annotation table |
| goa_cc_table | GOA cellular component annotation table |
| goa_mf_table | GOA molecular function annotation table |
| grapes-nin-grapes | not in |
| gwas_table | GWAS catalog table |
| hgnc_group_table | HGNC gene group annotation table |
| id_enriched_proteins | Identify enriched proteins |
| inweb_hash | InWeb hash table |
| italics | italics |
| launch_genoppi | launch genoppi |
| make_interactive | Make ggplot interactive using plotly |
| map_gene_id | Map Uniprot accession ID to gene name (HGNC symbol) |
| misc | misc tools |
| modify_ggplot_from_overlay | modify ggplot from overlay |
| msigdb_c1_table | MSigDB C1 collection (positional gene sets) annotation table |
| msigdb_c2_table | MSigDB C2 collection (curated gene sets) annotation table |
| msigdb_c3_table | MSigDB C3 collection (regulatory target gene sets) annotation... |
| msigdb_c4_table | MSigDB C4 collection (computational gene sets) annotation... |
| msigdb_c5_table | MSigDB C5 collection (GO gene sets) annotation table |
| msigdb_c6_table | MSigDB C6 collection (oncogenic signatures) annotation table |
| msigdb_c7_table | MSigDB C7 collection (immunologic signatures) annotation... |
| msigdb_h_table | MSigDB H collection (hallmark gene sets) annotation table |
| null_omit | omit nulls from list |
| plot_overlay | plot overlay |
| plot_scatter_basic | plot a basic scatte plot |
| plot_scatter_basic_all | plot a list of basic scatter plots |
| plot_volcano_basic | Plot basic volcano |
| read_input | Read input data |
| set_names_by_dataset | set_names_by_dataset |
| stop_invalid_columns | Stop invalid columns |
| subset_snp_loci | Subset SNP-to-gene list |
| theme_genoppi | Genoppi GG theme |
| theme_genoppi_bar | genoppi themed bar |
| to_overlay_data | to overlay data |
| validate_reference | validate reference data.frame |
| venn_to_table | venn diagram to table |
