Package index • pepitope

All functions

annotate_coding(): Annotate VCF variants with coding changes

annotate_fusions(): Aggregate fusion VCFs into a table

count_bc(): Count barcodes using guide-counter

demux_fq(): Use fqtk tool to demultiplex fastq files

filter_fusions(): Filter a fusion VRanges object by number of reads and tools

filter_variants(): Make results report to save as xlsx sheets (full, filtered, peptides)

make_peptides(): Make a variants report as named list of tables

make_report(): Make a variants report as named list of tables

pep_tile(): Tile cDNA into peptide sequences

pepitope-package pepitope: Pepitope: peptide epitopes from reference genome and variant (VCF) file

plot_barcode_overlap(): Plot barcode overlap between different samples

plot_distr(): Plot the read distribution across barcodes

plot_reads(): Plot the overall read counts

plot_screen(): Plot screen results

remove_cutsite(): Remove a Restriction Enzyme cut site but keep AA in a tiled peptide data.frame

screen_calc(): Calculate differential abundance of construct barcodes

subset_context(): Subset nucleotide/protein sequences to codon +/- 45 bp context

subset_context_fusion(): Subset the peptide context for gene fusions