annotate_mut_effect()
and ensuring that return of same column names in case of empty outputannotate_mut_effect()
generate_combined_dataset()
to multiple inputsannotate_mut_effect()
generate_combined_dataset()
in vignetteclass
was renamed to event_type
mut_id
, junc_id
, tx_id
, event_type
add_context_seq()
. the resulting context sequence covers the complete intron instead of the exon/intron boundary only. Instead of a the junction position in the cts_seq, the positions are given in form of an interval in the cts_junc_pos
column for intron retentions. (0,start_IR, end_IR, end_cts) add_peptide()
was adjusted for intron retentionsannotate_spliceai_junction()
that led to annotation with same transcript generate_junction_id()
junc2breakpoint()
breakpoint2junc()
bed_to_junc()
is_canonical()
is_in_rnaseq()
parse_gtf()
add_context_seq()
add_peptide()
add_peptide()
get_junc_pos()
modify_tx()
transform_for_requant
functionadd_tx()
modify_tx()
add_context_seq()
add_peptide()
parse_spliceai()
and format_spliceai()
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