API for ctl43/TranSpotteR
Pipeline for identifying LINE1 insertoin in the WGS data
| Global functions | |
|---|---|
| .add_back_seq | Source code |
| .check_polyA | Source code |
| .combined_rle | Source code |
| .filter_read_by_coverage | Source code |
| .get_TSD | Source code |
| .get_clip_length | Source code |
| .get_middle_unmapped_pos | Source code |
| .get_partner_read_id | Source code |
| .get_the_best | Source code |
| .initialize_storage | Source code |
| .internal_annotation | Source code |
| .internal_construction | Source code |
| .preprocess_info | Source code |
| .process_msa | Source code |
| .reorder_seq_info | Source code |
| .resolve_overlap | Source code |
| .simple_initialize_storage | Source code |
| anno_polyA | Source code |
| annotate_contigs | Man page Source code |
| annotate_seq | Man page Source code |
| assemble_reads | Man page Source code |
| bwa_alignment | Source code |
| cluster_reads | Man page Source code |
| construct_contigs | Man page Source code |
| convert_character2gr | Source code |
| convertingHtoS | Source code |
| cxx_query_to_reference_position | Source code |
| cxx_ref_extension | Source code |
| data_input | Source code |
| extract_element_at | Man page |
| extract_reads | Man page Source code |
| first_element | Man page Source code |
| get_unmapped_clipped_read | Source code |
| grl_to_character | Source code |
| how_many_regions_in_range | Source code |
| import_files | Man page Source code |
| infer_simple_insertion | Source code |
| infer_transposon | Source code |
| last_element | Man page Source code |
| merge_glist | Man page |
| merge_granges | Source code |
| msa_view | Source code |
| non_polyA_or_insert | Source code |
| non_targets | Source code |
| overlapper | Source code |
| pairing_annotation | Source code |
| read_aln_info | Source code |
| replcae_space | Source code |
| rle_to_cigar | Source code |
| sam2gr | Source code |
| simple_data_input | Source code |
| string_reverseComplement | Source code |
| t_coffee | Source code |
| unify_cigar_strand | Source code |
| which_is_fully_covered | Source code |
