Package: amplican 1.27.0

Eivind Valen

amplican: Automated analysis of CRISPR experiments

`amplican` performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.

Authors:Kornel Labun [aut], Eivind Valen [cph, cre]

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amplican.pdf |amplican.html✨
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NEWS

Peer review:

Bug tracker:https://github.com/valenlab/amplican/issues

On BioConductor:amplican-1.27.0(bioc 3.20)amplican-1.26.0(bioc 3.19)

bioconductor-package

51 exports 1.24 score 118 dependencies

Last updated 2 months agofrom:3451266981

Exports:AlignmentsExperimentSetamplican_print_readsamplicanAlignamplicanConsensusamplicanFilteramplicanMapamplicanNormalizeamplicanOverlapamplicanPipelineamplicanPipelineConservativeamplicanReportamplicanSummarizeassignedCountbarcodeDatabarcodeData<-cigarsToEventscomb_alongexperimentDataexperimentData<-extractEventsfindEOPfindLQRfindPDfwdReadsfwdReads<-fwdReadsTypefwdReadsType<-getEventsis_hdr_strictlookupAlignmentmetaplot_deletionsmetaplot_insertionsmetaplot_mismatchespairToEventsplot_cutsplot_deletionsplot_heightplot_heterogeneityplot_insertionsplot_mismatchesplot_variantsreadCountsreadCounts<-rveReadsrveReads<-rveReadsTyperveReadsType<-unassignedCountunassignedDataunassignedData<-writeAlignments

Dependencies:abindaskpassbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitopsbslibcachemcliclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDelayedArraydeldirdigestdplyrDTevaluateextrafontextrafontdbfansifarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2ggthemesgluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvhttrhwriterinterpIRangesisobandjpegjquerylibjsonliteknitrlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplyrpngpromisespurrrpwalignR6rappdirsRColorBrewerRcppRcppEigenRhtslibrlangrmarkdownRsamtoolsRttf2pt1S4ArraysS4VectorssassscalesShortReadsnowSparseArraystringistringrSummarizedExperimentsystibbletidyselecttinytexUCSC.utilsutf8vctrsviridisLitewafflewithrxfunXVectoryamlzlibbioc