Man pages for lagelab/Genoppi
genoppi
| accession_gene_table | Uniprot protein accession number to HGNC gene symbol mapping |
| add_plotly_layout_scatter | layout for scatterplot |
| add_plotly_layout_volcano | layout for volcano plot. |
| add_plotly_line_unity | add unity line |
| add_plotly_markers_search | search volcano plots |
| add_plotly_markers_search_pathway | search pathway plots |
| add_plotly_threshold_lines | add hover lines |
| add_plotly_trace | add genoppi trace |
| append_to_column | Append a string to a column |
| as.bait | as.bait |
| as.goi | as gene of interest |
| assign_color | assign color by column |
| assign_freq | assign frequency |
| bioplex_table | BioPlex protein-protein interactions |
| bold | bold |
| calc_cumsum_table | calculate the cumulative sum of frequencies |
| calc_fisher | Perform Fisher's exact test |
| calc_hyper | Perform hypergeometric test |
| calc_logfc_limit | calculate logfc limits |
| calc_mod_ttest | Perform one-sample moderated t-test |
| catf | warnings to stderr |
| check_input | Check proteomic 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 (1) |
| example_data2 | Example proteomic data (2) |
| example_data3 | Example proteomic data (3) |
| find_docs | find docs |
| genes_snps | 1000 Genomes SNP to HGNC gene symbol mapping |
| get_bioplex_list | Retrieve Bioplex 3.0 interactors for a given bait |
| get_gene_from_snp | get the genes that matches a vector of SNPs |
| get_gene_lists | Read in gene lists |
| get_geneset_overlay | get geneset as overlay |
| get_gg_legend | get ggplot legend |
| get_gwas_lists | Retreive GWAS catalog data for a given list of traits |
| get_inweb_list | Retrieve InWeb data for a given bait |
| get_irefindex_list | Retrieve irefindex for a given bait |
| get_overlay_df | get overlay data.frame |
| get_pathways | Retreive pathway annotations for a list of genes |
| get_replicate_summary_text | get replicate summary |
| get_shiny_errors | get shiny errors |
| get_snp_lists | Map SNP lists to genes |
| get_tissue_list | Retrieve Genotype-Tissue Expression (GTEx) or Human Protein... |
| get_tissue_lists | deprecated. See ?get_tissue_list |
| gnomad_table | gnomAD mutational constraint (pLI) annotations |
| goa_bp_table | GO biological process annotations |
| goa_cc_table | GO cellular component annotations |
| goa_mf_table | GO molecular function annotations |
| grapes-nin-grapes | not in |
| gtex_protein | GTEx protein tissue specificity annotations |
| gtex_rna | GTEx RNA tissue specificity annotations |
| gwas_table | NHGRI-EBI GWAS catalog genetic associations |
| hgnc_group_table | HGNC gene group annotations |
| hline | horizontal line |
| hpa_rna | Human Protein Atlas (HPA) RNA tissue specificity annotations |
| html_translate_significance_thresholds | translate significance and logfc thresholds to html text |
| hyperlink | hyperlink |
| id_enriched_proteins | Identify enriched proteins |
| id_significant_proteins | Identify significant proteins |
| inweb_table | InWeb protein-protein interactions |
| irefindex_table | iRefIndex protein-protein interactions |
| is_cols | is columns |
| italics | italics |
| lapply_calc_hyper | lapply calc_hyper to multiple datasets |
| launch_genoppi | launch genoppi |
| line_unity | line_unity |
| lun | length of unique |
| make_interactive | Make ggplot interactive using plotly |
| map_gene_id | Map Uniprot accession ID to gene name (HGNC symbol) |
| msigdb_c1_table | MSigDB C1 collection (positional gene sets) annotations |
| msigdb_c2_table | MSigDB C2 collection (curated gene sets) annotations |
| msigdb_c3_table | MSigDB C3 collection (regulatory target gene sets)... |
| msigdb_c4_table | MSigDB C4 collection (computational gene sets) annotations |
| msigdb_c5_table | MSigDB C5 collection (GO gene sets) annotations |
| msigdb_c6_table | MSigDB C6 collection (oncogenic signatures) annotations |
| msigdb_c7_table | MSigDB C7 collection (immunologic sig natures) annotations |
| msigdb_h_table | MSigDB H collection (hallmark gene sets) annotations |
| null_omit | omit nulls from list |
| parse_rd | parse documentation files for content |
| parse_uploaded_file | parse uploaded file |
| plotly_tissue_enrichment | plot tissue enrichment |
| plot_overlay | superimpose genesets onto plots |
| plot_scatter_basic | plot a basic scatter plot of replicates |
| plot_scatter_basic_all | plot a list of basic scatter plots |
| plot_tissue_enrichment | plot tissue enrichment |
| plot_venn | plot venn diagram |
| plot_volcano_basic | Plot basic volcano |
| read_input | Read in proteomic data from file |
| set_names_by_dataset | set_names_by_dataset |
| shape_to_symbol | translate ggplot shapes to plotly symbols |
| stop_invalid_columns | Stop invalid columns |
| strsplit.nchar | split string by character numbers |
| subset_snp_loci | Subset SNP-to-gene list |
| symbol_to_shape | translate plotly symbols to ggplot shapes |
| table_symbols | get table of plotly/ggplot symbols |
| tabulate_markers | tabulate markers |
| theme_genoppi_bar | genoppi themed bar |
| theme_scatter | volcano theme |
| theme_volcano | Volcano plot simple theme |
| theme_volcano_custom | volcano theme complex |
| to_overlay_data | to overlay data |
| validate_reference | validate reference data.frame |
| venn_to_table | venn diagram to table |
| vline | vertical line |
