amplican

DOI: 10.18129/B9.bioc.amplican    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see amplican.

Automated analysis of CRISPR experiments

Bioconductor version: 3.13

`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 "4.1") 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 1.14.0
In Bioconductor since BioC 3.6 (R-3.4) (4 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_1.14.0.tar.gz
Windows Binary amplican_1.14.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) amplican_1.14.0.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

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