Simplify the analysis and visualization of translated open reading frames (ORFs) using Ribo-Seq data.

Detecting translated ORFs within Ribo-Seq data often requires evaluating typical features of translation, such as triplet periodicity within P-site alignments. inspectorORF simplifies the task of visualising and evaluating ORFs with a flexible plotting API and extensive annotation support.

• Plot ORFs with RNA-Seq coverage and Ribo-Seq P-sites.
• Compare the same ORFs across multiple conditions or replicates.
• Add custom layers such as:
  • Mass-spec fragment hits
  • Kozak scores
  • Translation efficiency (TE)
• Visualise 5'/3' UTRs and annotate non-canonical start codons.
• Extract nucleotide and amino acid sequences from ORFs with ease.

Install Bioconductor dependencies -

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install(c("GenomeInfoDb", "S4Vectors", "plyranges", "bioseq", "Biostrings", "GenomicRanges", "rtracklayer"))

Install inspectorORF from GitHub:

# install.packages("devtools")
devtools::install_github("aylz83/inspectorORF")

• GenomeInfoDb
• S4Vectors
• tibble
• tidyr
• bioseq
• plyranges
• Biostrings
• data.table
• GenomicRanges
• ggh4x
• ggplot2
• ggrepel
• grid
• patchwork
• rtracklayer
• parallel
• dplyr
• methods
• stats
• grid

• Ribo-Seq and RNA-Seq data was processed from GEO accession GSE16214, aligned to Gencode V44 and subset for the NTN4 gene.
• Kozak scores calculated with ORFik.
• Proteomic and long-read data simulated for vignette example.

library(inspectorORF)

# Generate primary track data
tracks <- merge_RNA_tracks_with_ORFquant(
	rna_reads = system.file("example_data", "control_rna_tracks.bed.gz", package = "inspectorORF"),
	orfquant_psites = system.file("example_data", "control_psites_for_ORFquant", package = "inspectorORF")
)

# Extract transcript track data for transcript of interest
tx_tracks <- get_transcript_tracks(
	tracks,
	gtf_file = system.file("example_data", "annotation_subset.gtf", package = "inspectorORF"),
	genome_file = system.file("example_data", "chr12.2bit", package = "inspectorORF"),
	transcript_ids = c("ENST00000343702.9"), # multiple transcript ids supported
)

# Create a full transcript plot
transcript_plot(
	tx_tracks,
	transcript_filter = "ENST00000343702.9" # Requires 1 transcript at a time
)

# or, create an ORF plot from the coding region starting at transcript position 456
orf_plot(
	tx_tracks,
	transcript_filter = "ENST00000343702.9",
	start_position = 456
)

test data available within the example_data folder

• Continue work on removal of some unneccesary dependencies (dplyr)