Package index • pepitope

All functions

annotate_coding(): Annotate VCF variants with coding changes
annotate_fusions(): Aggregate fusion VCFs into a table
count_fastq(): Count barcodes directly from source 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_read_count() plot_reads(): Plot the overall read counts
plot_read_distr() plot_distr(): Plot the read distribution across barcodes
plot_read_structure(): Plot annotated read structure examples
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