amplican

This is the released version of amplican; for the devel version, see amplican.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6

Automated analysis of CRISPR experiments

Bioconductor version: Release (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")):

Kornel Labun. amplican: Automated analysis of CRISPR experiments. doi:10.18129/B9.bioc.amplican, R package version 1.34.0, https://bioconductor.org/packages/amplican.

Generated from the package metadata; it may differ from the package's own citation.

Installation

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, CRISPR, ImmunoOncology, Software, Technology, qPCR
Version	1.34.0
In Bioconductor since	BioC 3.6 (R-3.4) (9 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), data.table (>= 1.10.4-3), rmarkdown (>= 1.6), knitr (>= 1.16), cluster (>= 2.1.4), rlang (>= 1.2.0)
System Requirements
URL	https://github.com/valenlab/amplican
Bug Reports	https://github.com/valenlab/amplican/issues

Suggests	testthat, BiocStyle, GenomicAlignments
Linking To	Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	amplican_1.34.0.tar.gz
Windows Binary (x86_64)	amplican_1.34.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	amplican_1.34.0.tgz
macOS Binary (sonoma-arm64)	amplican_1.34.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/amplican
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/amplican
Package Short Url	https://bioconductor.org/packages/amplican/
Package Downloads Report	Download Stats