Man pages for Jeremy37/rgenie
Analysis of GenIE Experiments
| aligned_read_profile_plots | Returns a plot showing the aligned read profile of HDR and WT... |
| alignment_analysis | Alignment-based GenIE analysis |
| alignment_analysis_plots | Returns all main plots for a single alignment analysis... |
| alignment_summary_plot | Plots a summary of alignment analysis results for a single... |
| allele_effect_plot | Plots estimated effect sizes and confidence intervals for top... |
| atac_del_results | GenIE ATAC example rs7729529 alignment analysis results. |
| atac_grep_results | GenIE ATAC example rs7729529 grep results. |
| atac_regions | GenIE regions for the MUL1 example. |
| atac_replicates | GenIE replicates for the MUL1 example. |
| bind_results | Given results for rgenie grep or alignment analysis of a set... |
| deletion_alleles_plot | Plots unique deletion alleles and their "pileup" count... |
| deletion_profile_plot | Plots the deletion "pileup" profile separately for each... |
| download_example | Downloads example data for rgenie. |
| experiment_summary_plot | Plots a summary of genie results across multiple regions. |
| genie_plot_options | Returns a list with default options for all rgenie plots,... |
| get_variance_components | Performs a variance components estimate for each deletion... |
| grep_analysis | Grep-based GenIE analysis |
| grep_summary_plot | Plots a summary of genie results from a grep analysis. |
| mul1_del_results | GenIE alignment analysis results for the MUL1 example. |
| mul1_grep_results | GenIE grep results list. |
| mul1_regions | GenIE regions for the MUL1 example. |
| mul1_replicates | GenIE replicates for the MUL1 example. |
| power_analysis | Performs estimates of power to detect effects of alleles at... |
| power_plots | Returns a set of plots summarising the expected power to... |
| replicate_qc_plot | Plots quality control metrics for alignment analysis... |
| replicate_summary_plot | Plots a summary of alignment analysis replicates. |
| rgenie | rgenie: Analysis of GenIE experiments |
| variance_components_plot | Plots variance components estimates for all unique alleles. |
| write_results | Given results for rgenie grep or alignment analysis of a set... |
