amplican

DOI: 10.18129/B9.bioc.amplican    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see amplican.

Automated analysis of CRISPR experiments

Bioconductor version: 3.9

`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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

HTML		amplican FAQ
HTML	R Script	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
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, CRISPR, ImmunoOncology, Software, Technology, qPCR
Version	1.6.2
In Bioconductor since	BioC 3.6 (R-3.4) (2 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 (>= 2.2.0), 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), clusterCrit (>= 1.2.7)
LinkingTo	Rcpp
Suggests	testthat, BiocStyle, GenomicAlignments
SystemRequirements
Enhances
URL	https://github.com/valenlab/amplican
BugReports	https://github.com/valenlab/amplican/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	amplican_1.6.2.tar.gz
Windows Binary	amplican_1.6.2.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	amplican_1.6.2.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