amplican

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

Automated analysis of CRISPR experiments

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DOI: 10.18129/B9.bioc.amplican

Bioconductor version: Development (3.23)

`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 gmail.com>

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

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("amplican")

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

Documentation

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

browseVignettes("amplican")

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

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, CRISPR, ImmunoOncology, Software, Technology, qPCR

Version 1.33.1

In Bioconductor since BioC 3.6 (R-3.4) (8 years)

License GPL-3

Depends R (>= 3.5.0), methods, BiocGenerics(>= 0.22.0), Biostrings(>= 2.44.2), pwalign

Imports Rcpp, utils (>= 3.4.1), S4Vectors(>= 0.14.3), ShortRead(>= 1.34.0), IRanges(>= 2.10.2), GenomicRanges(>= 1.61.1), Seqinfo, BiocParallel(>= 1.10.1), gtable (>= 0.2.0), gridExtra (>= 2.2.1), ggplot2 (>= 3.3.4), ggthemes (>= 3.4.0), stringr (>= 1.2.0), stats (>= 3.4.1), matrixStats (>= 0.52.2), Matrix (>= 1.2-10), dplyr (>= 0.7.2), data.table (>= 1.10.4-3), rmarkdown (>= 1.6), knitr (>= 1.16), cluster (>= 2.1.4)

System Requirements

URL https://github.com/valenlab/amplican

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

Suggests testthat, BiocStyle, GenomicAlignments

Linking To Rcpp

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