To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("CrispRVariants")

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

CrispRVariants

 

   

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

Tools for counting and visualising mutations in a target location

Bioconductor version: Development (3.6)

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>

Citation (from within R, enter citation("CrispRVariants")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("CrispRVariants")

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, Software, VariantDetection, Visualization
Version 1.5.0
In Bioconductor since BioC 3.3 (R-3.3) (1 year)
License GPL-2
Depends R (>= 3.4), 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
Build Report  

Package Archives

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

Package Source CrispRVariants_1.5.0.tar.gz
Windows Binary CrispRVariants_1.5.0.zip
Mac OS X 10.11 (El Capitan) CrispRVariants_1.5.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/CrispRVariants
Package Short Url http://bioconductor.org/packages/CrispRVariants/
Package Downloads Report Download Stats

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