Automated analysis of CRISPR experiments

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Documentation for package ‘amplican’ version 1.20.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

amplican-package	Automated analysis of CRISPR experiments.
amplican	Automated analysis of CRISPR experiments.
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.
amplican_print_reads	Pretty print forward and reverse reads aligned to each other.
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.
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.
stat_bezier	Create quadratic or cubic bezier curves [copied from ggforce]