amplican                Automated analysis of CRISPR experiments.
amplican_print_reads    Pretty print forward and reverse reads aligned
                        to each other.
amplicanAlign           Align reads to amplicons.
amplicanConsensus       Extract consensus out of forward and reverse
                        events.
amplicanFilter          Filter Events Overlapping Primers, PRIMER
                        DIMERS and Low Alignment Score Events.
amplicanMap             Map events to their respective relative
                        coordinates specified with UPPER case.
amplicanNormalize       Remove events that can be found in Controls.
amplicanOverlap         Check which events overlap expected cut sites.
amplicanPipeline        Wraps main package functionality into one
                        function.
amplicanPipelineConservative
                        Wraps main package functionality into one
                        function.
amplicanReport          Prepare reports as .Rmd files.
amplicanSummarize       Summarize how many reads have frameshift and
                        how many reads have deletions.
cigarsToEvents          Transform extended CIGAR strings into GRanges.
comb_along              Generate all combinations along string
                        exchanging m characters at a time with
                        dictionary letters.
findEOP                 Find Events Overlapping Primers.
findLQR                 Find Off-targets and Fragmented alignments from
                        reads.
findPD                  Find PRIMER DIMER reads.
geom_bezier             Create quadratic or cubic bezier curves [copied
                        from ggforce]
getEvents               Transform aligned strings into GRanges
                        representation of events.
is_hdr_strict           Determine which reads conform to HDR using the
                        donor (strict, event-presence).
locate_pr_start         Find full or partial primer start positions
                        with mismatches.
metaplot_deletions      MetaPlots deletions using ggplot2.
metaplot_insertions     MetaPlots insertions using ggplot2.
metaplot_mismatches     MetaPlots mismatches using ggplot2.
pairToEvents            Read "pair" format of EMBOSS needle into
                        GRanges as events.
plot_cuts               Plots cuts using ggplot2.
plot_deletions          Plots deletions using ggplot2.
plot_height             Get figure height in inches for number of
                        elements on y axis.
plot_heterogeneity      Plots heterogeneity of the reads using ggplot2.
plot_insertions         Plots insertions using ggplot2.
plot_mismatches         Plots mismatches using ggplot2.
plot_variants           Plots most frequent variants using ggplot2.
waffle                  Create a Waffle Chart using ggplot2
