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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 (3.19)

`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.


Reference Manual PDF


biocViews Alignment, CRISPR, ImmunoOncology, Software, Technology, qPCR
Version 1.25.1
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), 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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