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amplican

Automated analysis of CRISPR experiments


Bioconductor version: Release (3.18)

`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 "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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

Details

biocViews Alignment, CRISPR, ImmunoOncology, Software, Technology, qPCR
Version 1.24.0
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), 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)
System Requirements
URL https://github.com/valenlab/amplican
Bug Reports https://github.com/valenlab/amplican/issues
See More
Suggests testthat, BiocStyle, GenomicAlignments
Linking To Rcpp
Enhances
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Build Report Build Report

Package Archives

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

Source Package amplican_1.24.0.tar.gz
Windows Binary amplican_1.24.0.zip (64-bit only)
macOS Binary (x86_64) amplican_1.24.0.tgz
macOS Binary (arm64) amplican_1.24.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/amplican
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/amplican
Bioc Package Browser https://code.bioconductor.org/browse/amplican/
Package Short Url https://bioconductor.org/packages/amplican/
Package Downloads Report Download Stats