Man pages for valenlab/amplican
Automated analysis of CRISPR experiments

AlignmentsExperimentSet-class	An S4 class to represent alignments from multiple experiments
alphabetQuality	This filters out sequences which have nonstandard...
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...
amplicanMap	Map events to their respective relative coordinates specified...
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.
amplican_print_reads	Pretty print forward and reverse reads aligned to each other.
amplicanReport	Prepare reports as .Rmd files.
amplicanSummarize	Summarize how many reads have frameshift and how many reads...
assignedCount	Get count of assigned reads.
barcodeData	Barcode data.
barcodeData-set	Barcode data.
checkConfigFile	Pre-process a config file and checks that everything is in...
checkFileWriteAccess	Checks if the given directory exist and can be written to.
checkPrimers	Checks if the forward and reverse primer are in the amplicon...
checkTarget	Checks if the guideRNA is in the amplicon.
cigarsToEvents	Transform extended CIGAR strings into GRanges.
comb_along	Generate all combinations along string exchanging m...
cumsumw	Cumulative sum to calculate shift
decode	Get codons for given string - translate
defGR	Helper to construct GRanges with additional metadata columns.
experimentData	Experiment data.
experimentData-set	Experiment data.
extractEvents	Extract AlignmentsExperimentSet events into data.frame.
findEOP	Find Events Overlapping Primers.
findLQR	Find Off-targets and Fragmented alignments from reads.
findPD	Find PRIMER DIMER reads.
flipRanges	Reverse complement events that have amplicons with direction...
fwdReads	Alignments for forward reads.
fwdReads-set	Alignments for forward reads.
fwdReadsType	Type of forward reads.
fwdReadsType-set	Read type for forward reads.
geom_bezier	Create quadratic or cubic bezier curves [copied from ggforce]
getEventInfo	This function takes alignments and gives back the events...
getEvents	Transform aligned strings into GRanges representation of...
get_left_primer	left primer sequence
get_right_primer	right primer sequence
get_seq	amplicon sequence, reverse complemented when needed
goodAvgQuality	This filters out sequences which have bad average quality...
goodBaseQuality	Filters out sequences which have bad base quality readings.
is_hdr_strict	Figure out which reads conform to the HDR using the donor.
lookupAlignment	Show alignment in human readable format.
makeAlignment	Make alignments helper.
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_amplicon	Plots amplicon sequence using ggplot2.
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.
readCounts	Alignments for forward reads.
readCounts-set	Alignments for forward reads.
revComp	Reverse and complement given string or list of strings
rveReads	Alignments for reverse reads.
rveReads-set	Alignments for forward reads.
rveReadsType	Type of reverse reads.
rveReadsType-set	Read type for reverse reads.
unassignedCount	Get count of unassigned reads.
unassignedData	Unassigned read information.
unassignedData-set	Alignments for forward reads.
upperGroups	Detect uppercases as ranges object.
writeAlignments	Write alignments to file.