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This is the development version of amplican; for the stable release version, see amplican.

Automated analysis of CRISPR experiments

Bioconductor version: Development (3.20)

`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")):


To install this package, start R (version "4.4") and enter:

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

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

amplican FAQ HTML
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 HTML R Script
Reference Manual PDF


biocViews Alignment, CRISPR, ImmunoOncology, Software, Technology, qPCR
Version 1.27.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL-3
Depends R (>= 3.5.0), methods, BiocGenerics(>= 0.22.0), Biostrings(>= 2.44.2), pwalign, 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 (>= 3.3.4), 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), cluster (>= 2.1.4)
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Suggests testthat, BiocStyle, GenomicAlignments
Linking To Rcpp
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package amplican_1.27.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) amplican_1.27.0.tgz
macOS Binary (arm64) amplican_1.27.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
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