Man pages for ilia-kats/RiboSeqTools
Tools for analysis of selective ribosome profiling (SeRP) data
| binding_scores | Calculate binding scores for each gene in a SeRP experiment |
| binom_ci | Calculate enrichment confidence interval. |
| binom_ci_profile | Calculate position-wise enrichment confidence intervals |
| defaults | Default parameters for a data set |
| downsample | Downsample all samples to the same total counts |
| fit_background_model | Fit a background model to a selective ribosome profiling data... |
| get_binding_positions | Extract statistically significant binding regions |
| get_binding_positions_by_threshold | Extract binding regions based on a threshold |
| get_elbow_threshold | Threshold data using the elbow method |
| get_genecounts | Calculate total read counts per gene |
| load_serp | Import ribosome profiling data |
| make_aligned_mats | Align data matrices |
| make_average_profilefun | Generate a default function for metagene profiles that... |
| make_enrichment_profilefun | Generate the default function for metagene enrichment... |
| make_expression_normalizefun | Generate the default function expression-normalized for... |
| make_label_fun | Create a mapping between experiment identifiers and names |
| metagene_profiles | Calculate metagene profiles |
| normalize | Perform library-size normalization |
| pipe | Pipe operator |
| plot_background_model | Quality control plots for background model estimation |
| plot_binding_positions | Plot binding regions |
| plot_metagene_profiles | Plot metagene profiles |
| plot.serp_data | Plot a profile along a gene |
| plot_treemap | Treemap plot of read counts per gene with an additional... |
| pois_ci | Calculate read counts confidence interval. |
| pois_ci_profile | Calculate position-wise confidence intervals |
| serp_data_accessors | Accessors for 'serp_data' objects |
| serp_feature_accessors | Accessors for 'serp_features' objects |
| serp_features | Create a 'serp_features' object |
| set_defaults | Set default parameters |
| test_binding | Statistical test for position-wise enrichment in selective... |
