CrispRVariants
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see CrispRVariants.
Tools for counting and visualising mutations in a target location
Bioconductor version: 3.19
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("CrispRVariants")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("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")| CrispRVariants | R Script | |
| CrispRVariants | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CRISPR, DataRepresentation, GeneticVariability, GenomicVariation, ImmunoOncology, Sequencing, Software, VariantDetection, Visualization |
| Version | 1.32.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8.5 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_1.32.0.tar.gz |
| Windows Binary (x86_64) | CrispRVariants_1.32.0.zip |
| macOS Binary (x86_64) | CrispRVariants_1.32.0.tgz |
| macOS Binary (arm64) | CrispRVariants_1.32.0.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 |