├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── RcppExports.R ├── class.R ├── codon-occupancy.R ├── enrichment-metagene.R ├── enzyme-digestion-sites.R ├── exporting-data.R ├── gene-expression-analysis.R ├── generic-methods.R ├── implementation-genome.R ├── implementation.R ├── metagene-plot.R ├── motif-logo.R ├── motif-occupancy.R ├── multiPeptide-occupancy.R ├── other-visualizations.R ├── pathway-enrichment-analysis.R ├── pausing-site-calculation.R ├── polarity-scores.R ├── preparing-transcripts.R ├── relative-motif-occupancy.R ├── riboTransVis-package.R ├── serp-binding-peaks-detection.R ├── serp-implementation-methods.R ├── serp-visualization.R ├── subset-data.R ├── upstream-workflows.R ├── utils.R ├── visualization-QC.R └── visualization-methods.R ├── README.md ├── inst └── extdata │ └── getSeq.py ├── man ├── TE_analysis.Rd ├── TE_differential_analysis.Rd ├── codon_occupancy_plot.Rd ├── codon_scatter_plot.Rd ├── construct_ribotrans.Rd ├── construct_serp.Rd ├── cor_plot.Rd ├── digestion_site_plot.Rd ├── do_boot.Rd ├── do_offset_correction.Rd ├── ecdf_plot.Rd ├── enrich_analysis.Rd ├── enrichment_metagene_plot.Rd ├── enrichment_plot1.Rd ├── enrichment_plot2.Rd ├── export_genome_occupancy-ribotrans-method.Rd ├── export_genome_occupancy.Rd ├── feature_plot.Rd ├── find_strong_peaks.Rd ├── find_weak_peaks.Rd ├── frame_plot.Rd ├── gene_differential_analysis.Rd ├── generate_kmers.Rd ├── generate_summary.Rd ├── genome_trans_plot.Rd ├── getCoverage.Rd ├── getCoverageGenome.Rd ├── getOccupancy.Rd ├── getOccupancyGenome.Rd ├── get_aa_table.Rd ├── get_codon_from_site.Rd ├── get_counts.Rd ├── get_coverage.Rd ├── get_log_ratio_mat.Rd ├── get_longest_transcript.Rd ├── get_normalized_reads.Rd ├── get_occupancy.Rd ├── get_pausing_sites.Rd ├── get_scaled_occupancy.Rd ├── get_transcript_sequence.Rd ├── length_plot.Rd ├── logo_plot.Rd ├── metagene_plot.Rd ├── motif_occupancy.Rd ├── multi_peptide_occupancy.Rd ├── peptide_scatter_plot.Rd ├── period_plot.Rd ├── pipe.Rd ├── plogo_plot.Rd ├── polarity_plot.Rd ├── prepareTransInfo.Rd ├── prepareTransInfo_forGenome.Rd ├── prepare_transcipt_file.Rd ├── pyExtractSeq.Rd ├── relative_dist_plot.Rd ├── relative_heatmap_plot.Rd ├── relative_motif_occupancy.Rd ├── relative_motif_plot.Rd ├── relative_offset_plot.Rd ├── ribotrans-class.Rd ├── serp-class.Rd ├── smoothEachPosition.Rd ├── subset_data.Rd ├── theme_ribo.Rd ├── to_position_matrix.Rd ├── trans_plot.Rd ├── trans_plot2.Rd ├── trim_adaptors.Rd ├── vocalno_plot.Rd └── whole_metagene_plot.Rd ├── riboTransVis.Rproj ├── src ├── Makevars ├── Makevars.win ├── RcppExports.cpp ├── RcppExports.o ├── boot_rcpp.cpp ├── boot_rcpp.o ├── riboTransVis.dll ├── rolling_window.cpp └── rolling_window.o └── vignettes ├── .gitignore ├── document.Rmd ├── ribotrans-workflow.png └── ribotransvis.png /.Rbuildignore: -------------------------------------------------------------------------------- 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