Package index

Package overview

splicelogic splicelogic-package

splicelogic: differential transcripts to splice events

Input preprocessing

preprocess()

Preprocess input GRanges object for splicing event calculation

prepare_exons()

Prepare exon ranges from a TxDb and DTU results table

prepare_exons_by_partition()

Prepare exons from two transcript partitions

Event detection

find_se() find_skipped_exons() find_ie() find_included_exons() find_mxe() find_mutually_exclusive_exons() find_ri() find_retained_introns() find_si() find_spliced_introns() find_a5ss() find_alternative_5_prime_splice_sites() find_a3ss() find_alternative_3_prime_splice_sites() find_atss() find_alternative_transcription_start_sites() find_ates() find_alternative_transcription_end_sites() find_all_events()

Find splice events from annotated exons

Plotting

plot_transcript_lfc()

Plot a per-transcript fold change for the transcripts of splicelogic events

plot_transcripts()

Plot the transcripts involved in splicelogic events

plot_transcripts_by_gene()

Plot the transcripts involved in splicelogic events, one plot per gene

plot_transcripts_by_pair()

Plot the transcripts involved in splicelogic events, one plot per pair

event_palette()

Default fill colours for splicelogic event types

Sequence extraction

get_seq()

Extract sequences for GRanges

Mock data generation

create_mock_data()

Create mock GRanges data for splicing event testing

generate_se() generate_mxe() generate_ri() generate_a5ss() generate_a3ss() generate_atss() generate_ates()

Generate mock splice events in a GRanges object