To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("amplican")

In most cases, you don't need to download the package archive at all.

amplican

DOI: 10.18129/B9.bioc.amplican    

Automated analysis of CRISPR experiments.

Bioconductor version: Release (3.6)

`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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("amplican")

Documentation

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, Software, Technology, qPCR
Version 1.0.0
License GPL-3
Depends R (>= 3.4.0), methods, BiocGenerics(>= 0.22.0), Biostrings(>= 2.44.2), data.table (>= 1.10.4)
Imports 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), ggbio(>= 1.24.1), 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
Suggests testthat, BiocStyle
SystemRequirements
Enhances
URL https://github.com/valenlab/amplican
BugReports https://github.com/valenlab/amplican/issues
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package amplican_1.0.0.tar.gz
Windows Binary amplican_1.0.0.zip
Mac OS X 10.11 (El Capitan) amplican_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/amplican
Package Short Url http://bioconductor.org/packages/amplican/
Package Downloads Report Download Stats

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