DOI: 10.18129/B9.bioc.amplican  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see amplican.

Automated analysis of CRISPR experiments

Bioconductor version: 3.16

`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.

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

Maintainer: Eivind Valen <eivind.valen at>

Citation (from within R, enter citation("amplican")):


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if (!require("BiocManager", quietly = TRUE))


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HTML amplican FAQ
HTML R Script amplican overview
HTML R Script example amplicon_report report
HTML R Script example barcode_report report
HTML R Script example group_report report
HTML R Script example guide_report report
HTML R Script example id_report report
HTML R Script example index report
PDF   Reference Manual
Text   NEWS


biocViews Alignment, CRISPR, ImmunoOncology, Software, Technology, qPCR
Version 1.20.0
In Bioconductor since BioC 3.6 (R-3.4) (5.5 years)
License GPL-3
Depends R (>= 3.5.0), methods, BiocGenerics(>= 0.22.0), Biostrings(>= 2.44.2), data.table (>= 1.10.4-3)
Imports Rcpp, utils (>= 3.4.1), S4Vectors(>= 0.14.3), ShortRead(>= 1.34.0), IRanges(>= 2.10.2), GenomicRanges(>= 1.28.4), GenomeInfoDb(>= 1.12.2), BiocParallel(>= 1.10.1), gtable (>= 0.2.0), gridExtra (>= 2.2.1), ggplot2 (>= 2.2.0), ggthemes (>= 3.4.0), waffle (>= 0.7.0), stringr (>= 1.2.0), stats (>= 3.4.1), matrixStats (>= 0.52.2), Matrix (>= 1.2-10), dplyr (>= 0.7.2), rmarkdown (>= 1.6), knitr (>= 1.16), clusterCrit (>= 1.2.7)
LinkingTo Rcpp
Suggests testthat, BiocStyle, GenomicAlignments
Depends On Me
Imports Me
Suggests Me
Links To Me
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Source Package amplican_1.20.0.tar.gz
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macOS Binary (x86_64) amplican_1.20.0.tgz
macOS Binary (arm64) amplican_1.20.0.tgz
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