Man pages for andrewGhazi/malacoda
Bayesian Analysis of High-Throughput Genomic Assays
| activities_example | Example activity measurements |
| barcode_by_id | Example barcode_allele_df |
| compute_activities | Compute MPRA activities |
| compute_kl_est | Compute KL divergence estimate |
| cond_prior_example | Example conditional prior |
| count_barcodes | Count barcodes |
| count_barcodes_in_fastq | Match barcodes for a single fastq |
| cut_out_seqs | Cut out sequence lines |
| decode_errors | Decode fastq |
| dropout_example | Example CRISPR dropout screen counts |
| example_posterior | Example posterior |
| example_result | Example output of fit_mpra_model |
| fastq_examples | Example FASTQ data |
| find_prior_weights | Find prior weights |
| fit_cond_prior | Fit a informative conditional prior |
| fit_dropout_model | Fit a Bayesian model of dropout CRISPR screen data |
| fit_grouped_prior | Fit priors by group |
| fit_marg_prior | Fit a marginal prior |
| fit_mpra_model | Fit a Bayesian MPRA model |
| fit_nb | Fit a negative binomial |
| generate_distance_matrix | Generate a distance matrix from a matrix of annotations |
| get_kl_divergences | Get Kullback-Leibler Divergences |
| get_label_y | Get ratio label y |
| get_prior_ratios | Evaluate prior ratios of MLE estimates |
| get_sample_correlations | Get MPRA sample correlations |
| get_sample_depths | Get Sample Depths |
| get_well_represented | Get well represented barcodes |
| increase_regularization | Increase a malacoda prior object's regularization |
| malacoda_intervals | Plot a variant's posterior intervals |
| malacoda-package | The 'malacoda' package. |
| marg_prior_example | Example marginal prior |
| mpra_tile_plot | Make a MPRA tile plot |
| plot_dna_representation | Plot DNA representation |
| plot_mpra_correlations | Plot MPRA sample correlations |
| plot_prior_ratios | Plot prior ratios |
| plot_prior_samples | Plot prior samples |
| plot_ratio_hexs | Create ratio by transcription shift hexbins |
| posterior_beeswarm | Create a posterior beeswarm plot |
| ratios_example | Example prior ratios object |
| run_activity_tests | Run MPRA activity tests |
| sample_from_prior | Sample from prior |
| score_annotation | Score an annotation source |
| summarise_cond_prior | Summarise a conditional prior |
| summarise_one_prior | Summarise one RNA prior |
| summarise_prior_samples | Summarise prior samples |
| trim_and_filter | Trim and Filter a FASTQ |
| u_deepsea | Example MPRA annotation set |
| umpra_example | Example MPRA counts from Ulirsch et al., 2016 |
