Man pages for valenlab/amplican
Automated analysis of CRISPR experiments

AlignmentsExperimentSet-classAn S4 class to represent alignments from multiple experiments
alphabetQualityThis filters out sequences which have nonstandard...
amplicanAutomated analysis of CRISPR experiments.
amplicanAlignAlign reads to amplicons.
amplicanConsensusExtract consensus out of forward and reverse events.
amplicanFilterFilter Events Overlapping Primers, PRIMER DIMERS and Low...
amplicanMapMap events to their respective relative coordinates specified...
amplicanNormalizeRemove events that can be found in Controls.
amplicanOverlapCheck which events overlap expected cut sites.
amplicanPipelineWraps main package functionality into one function.
amplican_print_readsPretty print forward and reverse reads aligned to each other.
amplicanReportPrepare reports as .Rmd files.
amplicanSummarizeSummarize how many reads have frameshift and how many reads...
assignedCountGet count of assigned reads.
barcodeDataBarcode data.
barcodeData-setBarcode data.
checkConfigFilePre-process a config file and checks that everything is in...
checkFileWriteAccessChecks if the given directory exist and can be written to.
checkPrimersChecks if the forward and reverse primer are in the amplicon...
checkTargetChecks if the guideRNA is in the amplicon.
cigarsToEventsTransform extended CIGAR strings into GRanges.
comb_alongGenerate all combinations along string exchanging m...
cumsumwCumulative sum to calculate shift
decodeGet codons for given string - translate
defGRHelper to construct GRanges with additional metadata columns.
experimentDataExperiment data.
experimentData-setExperiment data.
extractEventsExtract AlignmentsExperimentSet events into data.frame.
findEOPFind Events Overlapping Primers.
findLQRFind Off-targets and Fragmented alignments from reads.
findPDFind PRIMER DIMER reads.
flipRangesReverse complement events that have amplicons with direction...
fwdReadsAlignments for forward reads.
fwdReads-setAlignments for forward reads.
fwdReadsTypeType of forward reads.
fwdReadsType-setRead type for forward reads.
get_ampliconamplicon sequence, reverse complemented when needed
getEventInfoThis function takes alignments and gives back the events...
getEventsTransform aligned strings into GRanges representation of...
get_left_primerleft primer sequence
get_right_primerright primer sequence
goodAvgQualityThis filters out sequences which have bad average quality...
goodBaseQualityFilters out sequences which have bad base quality readings.
lookupAlignmentShow alignment in human readable format.
makeAlignmentMake alignments helper.
metaplot_deletionsMetaPlots deletions using ggplot2.
metaplot_insertionsMetaPlots insertions using ggplot2.
metaplot_mismatchesMetaPlots mismatches using ggplot2.
pairToEventsRead "pair" format of EMBOSS needle into GRanges as events.
plot_ampliconPlots amplicon sequence using ggplot2.
plot_cutsPlots cuts using ggplot2.
plot_deletionsPlots deletions using ggplot2.
plot_heightGet figure height in inches for number of elements on y axis.
plot_heterogeneityPlots heterogeneity of the reads using ggplot2.
plot_insertionsPlots insertions using ggplot2.
plot_mismatchesPlots mismatches using ggplot2.
plot_variantsPlots most frequent variants using ggplot2.
readCountsAlignments for forward reads.
readCounts-setAlignments for forward reads.
revCompReverse and complement given string or list of strings
rveReadsAlignments for reverse reads.
rveReads-setAlignments for forward reads.
rveReadsTypeType of reverse reads.
rveReadsType-setRead type for reverse reads.
unassignedCountGet count of unassigned reads.
unassignedDataUnassigned read information.
unassignedData-setAlignments for forward reads.
upperGroupsDetect uppercases as ranges object.
writeAlignmentsWrite alignments to file.
valenlab/amplican documentation built on June 18, 2018, 6:04 a.m.