Man pages for jeffkimbrel/MappgeneSummary
Summarize Mappgene SNV Data
| add_SNV | Add a column with SNV data |
| add_zika_reference | Add data for processed Zika peptides |
| copy_summary_template | Copy Summary Rmd Template |
| example_df_A_ivar | Example iVar snpSIFT dataframes A |
| example_df_A_lofreq | Example iVar, lofreq snpSIFT dataframes A |
| example_df_B_ivar | Example iVar snpSIFT dataframes B |
| example_df_B_lofreq | Example iVar, lofreq snpSIFT dataframes B |
| example_df_C_ivar | Example iVar snpSIFT dataframes C |
| example_df_C_lofreq | Example iVar, lofreq snpSIFT dataframes C |
| get_country_outbreak_info | Country data from outbreak API |
| get_coverages | Make coverage files from folder with bedgraphs |
| get_global_outbreak_info | Global data from outbreak API |
| get_outbreak_info | Data from outbreak API |
| get_outbreak_latest | Get most recent dates and proportions from outbreak API data |
| get_outbreak_peak | Get peak dates and proportions from outbreak API data |
| get_outbreak_start | Get start dates and proportions from outbreak API data |
| get_state_outbreak_info | State data from outbreak API |
| gini_simpson | Calculate the Gini-Simpson index for a set of frequencies |
| hill_12I | Calculate Hill numbers of order 1, 2, and Inf from a matrix |
| make_venn | Make Pipeline Venn |
| parse_ref_alt | Parse REF and ALT AA Characters |
| plot_coverage_ecdf | Plot ECDF coverage |
| plot_effect_counts | Barchart summary of the SNPsift Effects |
| plot_heatmap | Plot Heatmap of Specific Gene |
| plot_nmds | Plot NMDS of AF values |
| plot_outbreak_milestones | Get the first, peak and most recent times and plots for a... |
| plot_outbreak_trends | Plot trend data by location from outbreak API |
| read_mappgene_data | Load the mappgene data into a tibble |
| simpson | Calculate the Simpson index for a set of frequencies |
| view_HGVS_C | View HGVS_C Effects |
| zika_reference | Zika genome coordinates reference |
