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amplican

This is the development version of amplican; for the stable release version, see amplican.

Automated analysis of CRISPR experiments


Bioconductor version: Development (3.19)

`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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("amplican")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews Alignment, CRISPR, ImmunoOncology, Software, Technology, qPCR
Version 1.25.1
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
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Suggests testthat, BiocStyle, GenomicAlignments
Linking To Rcpp
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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/
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