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_pkgdown.yml
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_pkgdown.yml
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url: https://tron-bioinformatics.github.io/splice2neo/
reference:
- title: "Parse SpliceAI"
desc: "Functions to parse SpliceAI and CI-SpliceAI output into standard splice junction format"
- contents:
- parse_spliceai
- parse_spliceai_thresh
- parse_cispliceai_thresh
- format_spliceai
- format_spliceai_thresh
- format_cispliceai_thresh
- annotate_mut_effect
- title: "Parse MMsplice"
desc: "Functions to parse MMsplice output into standard splice junction format"
- contents:
- parse_mmsplice
- annotate_mmsplice
- get_exon_inclusion_junction
- get_exon_skipping_junction
- unique_junc_mmsplice
- title: "Parse Pangolin"
desc: "Functions to parse Pangolin output into standard splice junction format"
- contents:
- parse_pangolin
- format_pangolin
- annotate_mut_effect
- title: "Parse LeafCutter"
desc: "Functions to parse LeafCutter output into standard splice junction format"
- contents:
- import_leafcutter_counts
- leafcutter_transform
- transform_leafcutter_counts
- title: "Parse Regtools"
desc: "Functions to parse Regtools output into standard splice junction format"
- contents:
- import_regtools_junc
- regtools_transform
- transform_regtools_junc
- title: "Parse SplAdder"
desc: "Functions to parse SplAdder output into standard splice junction format"
- contents:
- import_spladder
- spladder_transform
- spladder_transform_format
- spladder_transform_ass
- spladder_transform_intron_retention
- spladder_transform_mutex_exon
- spladder_transform_exon_skipping
- title: "Parse IRfinder"
desc: "Functions to parse IRfinder output into standard splice junction format"
- contents:
- import_irfinder_txt
- filter_irfinder_txt
- parse_irfinder_txt
- transform_irfinder_txt
- title: "Parse SUPPA2"
desc: "Functions to parse SUPPA2 output into standard splice junction format"
- contents:
- read_suppa_ioe
- transform_suppa_se_events
- transform_suppa_ir_events
- transform_suppa_ass_events
- transform_suppa_mxe_events
- suppa_transform_format
- suppa_import
- suppa_transform
- title: "Parse STAR"
desc: "Functions to parse STAR SJ.out.tab into standard splice junction format"
- contents:
- parse_star_sj
- title: "Parse StringTie"
desc: "Functions to parse StringTie into standard splice junction format"
- contents:
- import_stringtie_gtf
- stringtie_transform_format
- stringtie_transform
- title: "Parse other formats"
desc: "Functions to parse otherformats into standard splice junction format"
- contents:
- bed_to_junc
- title: "Annotate"
desc: "Functions to annotate splice junctions"
- contents:
- add_tx
- add_context_seq
- modify_tx
- get_junc_pos
- get_intronretention_genomic_alt_pos
- get_unknown_exon_intron_retention
- add_peptide
- seq_truncate_nonstop
- exon_in_intron
- is_start_on_exon
- choose_tx
- title: "Requantification"
desc: "Functions for read support re-quantification with easyquant"
- contents:
- ends_with("_requant")
- title: "Canonical"
desc: "Functions annotate and filter for cnaonical splicing"
- contents:
- parse_gtf
- canonical_junctions
- is_canonical
- title: "ID transformation"
desc: "Functions to generate and transform ids"
- contents:
- generate_junction_id
- breakpoint2junc
- junc2breakpoint
- liftover_junc_id
- title: "Merge and filter"
desc: "Functions annotate and filter for canonical splicing"
- contents:
- unique_mut_junc
- is_in_rnaseq
- combine_mut_junc
- add_identified_in_RNA
- generate_combined_dataset
- title: "Others"
desc: "Other functions"
- contents:
- junc_to_gr
- get_intronretention_alt_pos
- next_junctions
- sort_columns
- unsorted_junc_df
- pangolin_effect_translation
- title: "Data"
desc: "Toy example datasets"
- contents:
- starts_with("toy_")
- unsorted_junc_df
- canonical_juncs