CrispRVariants

DOI: 10.18129/B9.bioc.CrispRVariants    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see CrispRVariants.

Tools for counting and visualising mutations in a target location

Bioconductor version: 3.8

CrispRVariants provides tools for analysing the results of a CRISPR-Cas9 mutagenesis sequencing experiment, or other sequencing experiments where variants within a given region are of interest. These tools allow users to localize variant allele combinations with respect to any genomic location (e.g. the Cas9 cut site), plot allele combinations and calculate mutation rates with flexible filtering of unrelated variants.

Author: Helen Lindsay [aut, cre]

Maintainer: Helen Lindsay <helen.lindsay at uzh.ch>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("CrispRVariants")

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("CrispRVariants")

 

PDF	R Script	CrispRVariants
PDF		Reference Manual
Text		NEWS

Details

biocViews	CRISPR, DataRepresentation, GeneticVariability, GenomicVariation, ImmunoOncology, Software, VariantDetection, Visualization
Version	1.10.1
In Bioconductor since	BioC 3.3 (R-3.3) (3 years)
License	GPL-2
Depends	R (>= 3.5), ggplot2 (>= 2.2.0)
Imports	AnnotationDbi, BiocParallel, Biostrings, methods, GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices, grid, gridExtra, IRanges, reshape2, Rsamtools, S4Vectors(>= 0.9.38), utils
LinkingTo
Suggests	BiocStyle, gdata, GenomicFeatures, knitr, rmarkdown, rtracklayer, sangerseqR, testthat, VariantAnnotation
SystemRequirements
Enhances
URL
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	CrispRVariants_1.10.1.tar.gz
Windows Binary	CrispRVariants_1.10.1.zip
Mac OS X 10.11 (El Capitan)	CrispRVariants_1.10.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CrispRVariants
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CrispRVariants
Package Short Url	http://bioconductor.org/packages/CrispRVariants/
Package Downloads Report	Download Stats