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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 (3.19)

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 chuv.ch>

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

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("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")
CrispRVariants PDF R Script
CrispRVariants HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CRISPR, DataRepresentation, GeneticVariability, GenomicVariation, ImmunoOncology, Sequencing, Software, VariantDetection, Visualization
Version 1.31.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL-2
Depends R (>= 4.3.0), ggplot2 (>= 2.2.0)
Imports AnnotationDbi, BiocParallel, Biostrings, methods, GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices, grid, gridExtra, IRanges, reshape2, Rsamtools, S4Vectors(>= 0.9.38), utils
System Requirements
URL
See More
Suggests BiocStyle, GenomicFeatures, knitr, rmarkdown, readxl, rtracklayer, sangerseqR, testthat, VariantAnnotation
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package CrispRVariants_1.31.0.tar.gz
Windows Binary CrispRVariants_1.31.0.zip
macOS Binary (x86_64) CrispRVariants_1.31.0.tgz
macOS Binary (arm64) CrispRVariants_1.31.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CrispRVariants
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CrispRVariants
Bioc Package Browser https://code.bioconductor.org/browse/CrispRVariants/
Package Short Url https://bioconductor.org/packages/CrispRVariants/
Package Downloads Report Download Stats