Package: amplican 1.29.0

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✨
amplican/json (API)
NEWS

# Install 'amplican' in R:
install.packages('amplican', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:amplican-1.29.0(bioc 3.21)amplican-1.28.0(bioc 3.20)

immunooncologytechnologyalignmentqpcrcrisprcpp

7.66 score 10 stars 41 scripts 346 downloads 51 exports 117 dependencies

Last updated 3 months agofrom:555fe1ea6b. Checks:1 OK, 8 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 01 2025
R-4.5-win-x86_64NOTEJan 01 2025
R-4.5-linux-x86_64NOTEJan 01 2025
R-4.4-win-x86_64NOTEJan 01 2025
R-4.4-mac-x86_64NOTEJan 01 2025
R-4.4-mac-aarch64NOTEJan 01 2025
R-4.3-win-x86_64NOTEJan 01 2025
R-4.3-mac-x86_64NOTEJan 01 2025
R-4.3-mac-aarch64NOTEJan 01 2025

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.utilsutf8vctrsviridisLitewafflewithrxfunXVectoryaml

ampliCan FAQ

Kornel Labun & Eivind Valen

Rendered fromamplicanFAQ.Rmdusingknitr::rmarkdownon Jan 01 2025.

Last update: 2023-05-02
Started: 2018-09-14

ampliCan Overview

Kornel Labun & Eivind Valen

Rendered fromamplicanOverview.Rmdusingknitr::rmarkdownon Jan 01 2025.

Last update: 2024-04-24
Started: 2016-08-23

Report breakdown by amplicon sequence

ampliCan

Rendered fromexample_amplicon_report.Rmdusingknitr::rmarkdownon Jan 01 2025.

Last update: 2023-05-02
Started: 2017-06-02

Report breakdown by barcode

ampliCan

Rendered fromexample_barcode_report.Rmdusingknitr::rmarkdownon Jan 01 2025.

Last update: 2023-05-02
Started: 2017-06-02

Report breakdown by group

ampliCan

Rendered fromexample_group_report.Rmdusingknitr::rmarkdownon Jan 01 2025.

Last update: 2023-07-30
Started: 2017-06-02

Report breakdown by guideRNA

ampliCan

Rendered fromexample_guide_report.Rmdusingknitr::rmarkdownon Jan 01 2025.

Last update: 2023-07-30
Started: 2017-06-02

Report breakdown by ID

ampliCan

Rendered fromexample_id_report.Rmdusingknitr::rmarkdownon Jan 01 2025.

Last update: 2023-05-02
Started: 2017-06-02

Summary Read Report

ampliCan

Rendered fromexample_index.Rmdusingknitr::rmarkdownon Jan 01 2025.

Last update: 2023-05-02
Started: 2017-04-20

Readme and manuals

Help Manual

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