Splice-aware Quantification of ORF translation

Documentation for package ‘ORFquant’ version 1.1.0

annotate_ORFs	Annotate detected ORFs in transcript and genome space
annotate_splicing	Annotate splice features of detected ORFs
calc_orf_pval	Collect ORF Ribo-seq statistics
create_ORFquant_html_report	Create an html report summarizing ORFquant results
detect_readthrough	Analyzed translation on possible readthrough regions (beta)
detect_translated_orfs	Detect actively translated ORFs
from_tx_togen	Map transcript coordinates to genomic coordinates
get_orfs	Find ATG-starting ORFs in a sequence
get_ps_fromsplicemin	Offset spliced reads on minus strand
get_ps_fromspliceplus	Offset spliced reads on plus strand
get_reathr_seq	Extract possible readthrough sequences (beta)
load_annotation	Load genomic features and genome sequence
ORFquant	Detection, quantification and annotation of translated ORFs in a genomic region
plot_ORFquant_results	Plot general statistics about ORFquant results
prepare_annotation_files	Prepare comprehensive sets of annotated genomic features
prepare_for_ORFquant	Prepare the "for_ORFquant" file
run_ORFquant	Run the ORFquant pipeline
select_quantify_ORFs	Select and quantify ORF translation
select_start	Select start codon
select_txs	Select a subset of transcripts with Ribo-seq data
take_Fvals_spect	Extract output from multitaper analysis of a signal