API for Snitkin-Lab-Umich/regentrans
A framework and R package for using genomics to study regional pathogen transmission
| Global functions | |
|---|---|
| %>% | Man page |
| aln | Man page |
| aln_mini | Man page |
| check_allele_freq_input | Source code |
| check_bootstrap | Source code |
| check_control_labels | Source code |
| check_dists | Source code |
| check_dists_vs_locs | Source code |
| check_dna_bin | Source code |
| check_facility_fsp_input | Source code |
| check_fasta_vs_locs | Source code |
| check_find_major_alleles_input | Source code |
| check_get_clusters_inputs | Source code |
| check_get_frac_intra_input | Source code |
| check_get_largest_subtree_input | Source code |
| check_get_pair_types_input | Source code |
| check_get_patient_flow_input | Source code |
| check_locs | Source code |
| check_long_form_input | Source code |
| check_make_meta_seqs_input | Source code |
| check_merge_inter_summaries_input | Source code |
| check_pair_types | Source code |
| check_paths | Source code |
| check_pt | Source code |
| check_pt_trans_df | Source code |
| check_pt_vs_locs | Source code |
| check_pureness | Source code |
| check_reverse_list_str_input | Source code |
| check_subset_pairs_input | Source code |
| check_subtrs | Source code |
| check_subtrs_vs_isolate_labs | Source code |
| check_summarize_pairs_input | Source code |
| check_thresh | Source code |
| check_tr_vs_locs | Source code |
| check_tree | Source code |
| check_within_pop_var_inputs | Source code |
| days_between_isolates | Man page |
| dists | Man page |
| dists_mini | Man page |
| facil_coord | Man page |
| fill_missing_src_dest | Source code |
| find_major_alleles | Source code |
| fsp | Man page |
| get_allele_freq_btwn | Source code |
| get_allele_freq_within | Source code |
| get_clusters | Man page Source code |
| get_frac_intra | Man page Source code |
| get_genetic_flow | Man page Source code |
| get_indirect_flow | Source code |
| get_largest_subtree | Source code |
| get_pair_types | Man page Source code |
| get_patient_flow | Man page Source code |
| get_within_pop_var | Source code |
| make_long_form | Man page Source code |
| make_meta_seqs | Source code |
| merge_inter_summaries | Man page Source code |
| metadata | Man page |
| metadata_mini | Man page |
| pt_flow | Man page |
| pt_trans_df | Man page |
| reexports | Man page |
| reverse_list_str | Source code |
| subset_pairs | Source code |
| summarize_pairs | Man page Source code |
| tr | Man page |
| tr_mini | Man page |
