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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CrispRVariants")
In most cases, you don't need to download the package archive at all.
CrispRVariants
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This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see CrispRVariants.
Tools for counting and visualising mutations in a target location
Bioconductor version: 3.3
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("https://bioconductor.org/biocLite.R")
biocLite("CrispRVariants")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CrispRVariants")
| R Script | CrispRVariants | |
| Reference Manual |
Details
| biocViews | DataRepresentation, GeneticVariability, GenomicVariation, Software, VariantDetection, Visualization |
| Version | 1.0.2 |
| In Bioconductor since | BioC 3.3 (R-3.3) (< 6 months) |
| License | GPL-2 |
| Depends | R (>= 3.3), ggplot2 |
| 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_1.0.2.tar.gz |
| Windows Binary | CrispRVariants_1.0.2.zip |
| Mac OS X 10.9 (Mavericks) | CrispRVariants_1.0.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/CrispRVariants/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/CrispRVariants/ |
| Package Downloads Report | Download Stats |
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