Man pages for TRON-Bioinformatics/splice2neo
Aberrant splice junction analysis with associated mutations
| add_context_seq | Annotate splice junctions with resulting transcript sequence |
| add_identified_in_RNA | This is a wrapper function to directly map the information if... |
| add_peptide | Annotate splice junctions with resulting CDS and peptide... |
| add_tx | Annotate splice junctions with all possible transcript IDs in... |
| annotate_exon_idx | Annotate splice junctions- transcripts combination and... |
| annotate_junc_in_orf | Tests if junction position is in ORF... |
| annotate_mmsplice | Annotates the mmsplice output with additional columns... |
| annotate_mut_effect | Annotate splice variants effects with resulting junctions |
| annotate_truncated_cds | Tests if junction leads to truncated mutated gene product... |
| bed_to_junc | Transform a bed file into junction format |
| breakpoint2junc | Transforms breakpoint IDs (BPID) with given transcription... |
| canonical_juncs | A tibble with canonical junctions and their source (comma,... |
| canonical_junctions | Build canonical junctions from transcripts |
| choose_tx | Select a subset of transcripts per junction that are more... |
| classify_junc_tx | Classify splice junctions- transcripts combinations based on... |
| combine_mut_junc | Combines data sets with junctions from several different... |
| effect_to_junction_rules | Rules on how a splicing affecting variant creates a junction |
| effect_to_junction_rules_wo_ir | Rules on how a splicing affecting variant creates a junction... |
| exon_in_intron | Annotate if there is an exon within an intron |
| filter_irfinder_txt | Filter IRFinder intermediate table to remove likely false... |
| format_cispliceai_thresh | Formats CI-SpliceAI with -t flag output and filter for... |
| format_pangolin | Formats pangolin output and filter for predicted effects |
| format_spliceai | Formats spliceAI output and filter for predicted effects |
| format_spliceai_thresh | Formats SpliceAI with -T flag output and filter for predicted... |
| generate_combined_dataset | Combines tibbles with junctions from any number of RNA-seq... |
| generate_junction_id | Given the chromosome, junction start, junction end and... |
| get_exon_inclusion_junction | Compute the resulting junctions (junc_id) for exon inclusion... |
| get_exon_skipping_junction | Compute the resulting junction (junc_id) for exon skipping of... |
| get_intronretention_alt_pos | Get the alternative position of input junction from an intron... |
| get_intronretention_genomic_alt_pos | Get the alternative position of input junction from an intron... |
| get_junc_pos | Get the position of input junction in the transcript... |
| get_normalized_protein_junc_pos | Annotate the normalized junction position in the protein,... |
| get_peptide_context | Get peptide context sequence given a tibble with... |
| get_unknown_exon_intron_retention | Get the exon range flanking the other side of an intron... |
| import_irfinder_txt | Imports tabular IRFinder retained introns predictions |
| import_leafcutter_counts | Imports "_perind.counts.gz" from LeafCutter output. |
| import_regtools_junc | Imports Regtools junctions annotate table |
| import_spladder | Imports SplAdder output from a given path with... |
| import_star_sj | Imports tabular STAR SJ.out.tab splice junctions |
| import_stringtie_gtf | Imports StringTie GTF file |
| is_canonical | test if junction is canonical junction |
| is_first_reading_frame | Determine if transcript is in first reading frame, given a... |
| is_in_rnaseq | test if junction was found in corresponding RNA-seq data |
| is_start_on_exon | Tests if start or and end of junc is on exon. |
| junc2breakpoint | Transforms the junction id into the breakpoint id of the... |
| junc_to_gr | Convert a splice junction ID into a GRanges object |
| leafcutter_transform | Imports "*perind.counts.gz" from LeafCutter output and... |
| liftover_junc_id | LiftOver junction IDs using the liftOver tool |
| map_requant | Maps the re-quantification result from EasyQuant. on the... |
| modify_tx | Modify transcript by introducing splice junctions |
| next_junctions | Get genomic coordinates of possible next donor and acceptor... |
| pangolin_effect_translation | This dataset translates the increase/decrease splicing score... |
| parse_cispliceai_thresh | Parse VCF output file from CI-SpliceAI with -t flag as table |
| parse_gtf | Parse a GFF/GTF file as 'GRangesList' of exons |
| parse_irfinder_txt | Imports "IRFinder-IR-nondir.txt" from IRFinder short mode and... |
| parse_mmsplice | Parse .csv file from MMsplice output as data.frame |
| parse_pangolin | Parse VCF output file from pangolin as table |
| parse_spliceai | Parse VCF output file from spliceAI as table |
| parse_spliceai_thresh | Parse VCF output file from SpliceAI with -T flag as table |
| parse_star_sj | Imports "*SJ.out.tab" from STAR and transforms the raw output... |
| pipe | Pipe operator |
| read_requant | Imports the re-quantification results from analysis with... |
| read_suppa_ioe | Imports "_strict.ioe" from SUPPA2 output. |
| regtools_transform | Imports Regtools junctions annotate output and transforms the... |
| seq_truncate_nonstop | Truncate input sequence after input position before next stop... |
| sort_columns | Sorts columns of junction output file in the following order:... |
| spladder_transform | Imports SplAdder output from a given path and transforms it... |
| spladder_transform_ass | Transforms events from alternative 3' or 5' splice sites from... |
| spladder_transform_exon_skipping | Transforms events resulting from exon skipping from SplAdder... |
| spladder_transform_format | Transforms SplAdder output into standardized junction format |
| spladder_transform_intron_retention | Transforms events resulting from intron retention from... |
| spladder_transform_mutex_exon | Transforms events resulting from mutually exclusive exons... |
| stringtie_transform | Imports StringTie assembled transcripts and transforms the... |
| stringtie_transform_format | Transforms StringTie intermediate table into standardized... |
| suppa_import | Imports SUPPA2 output from a given path with "_strict.ioe"... |
| suppa_transform | Imports SUPPA2 output from a given path and transforms it... |
| suppa_transform_format | Transforms SUPPA2 ioe event files file into standardized... |
| toy_cds | An example CDS annotation GRangesList from a subset of human... |
| toy_junc_df | An example dataset of 18 splice junctions from human (hg19)... |
| toy_junc_id | An example dataset of 18 splice junctions in 'junc_id' format... |
| toy_junc_id_enst | An example dataset of 18 transcript IDs matching to the... |
| toy_transcripts | An example transcript annotation GRangesList from a subset of... |
| toy_transcripts_gr | An example dataset of full transcript ranges from a subset of... |
| transform_for_requant | Creates a table with context sequences for re-quantification... |
| transform_irfinder_txt | Transforms IRFinder intermediate table into standardized... |
| transform_leafcutter_counts | Transforms LeafCutter counts file into standardized junction... |
| transform_regtools_junc | Transforms Regtools intermediate files into standardized... |
| transform_star_sj | Transforms STAR intermediate table into standardized junction... |
| transform_suppa_ass_events | Transforms events from alternative 3' or 5' splice sites from... |
| transform_suppa_ir_events | Transforms events resulting from intron retention from SUPPA2... |
| transform_suppa_mxe_events | Transforms events resulting from mutually exclusive exons... |
| transform_suppa_se_events | Transforms events resulting from exon skipping from SUPPA2... |
| unique_junc_mmsplice | Filter junction datasets for unique 'mut_id', 'junc_id',... |
| unique_mut_junc | Filter junctions for unique combinations of mutation,... |
| unsorted_junc_df | A tibble in junction format but unsorted columns |
