crisprBase
Base functions and classes for CRISPR gRNA design
Bioconductor version: Release (3.19)
Provides S4 classes for general nucleases, CRISPR nucleases, CRISPR nickases, and base editors.Several CRISPR-specific genome arithmetic functions are implemented to help extract genomic coordinates of spacer and protospacer sequences. Commonly-used CRISPR nuclease objects are provided that can be readily used in other packages. Both DNA- and RNA-targeting nucleases are supported.
Author: Jean-Philippe Fortin [aut, cre]
Maintainer: Jean-Philippe Fortin <fortin946 at gmail.com>
citation("crisprBase")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("crisprBase")
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("crisprBase")| Introduction to crisprBase | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CRISPR, FunctionalGenomics, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2.5 years) |
| License | MIT + file LICENSE |
| Depends | utils, methods, R (>= 4.1) |
| Imports | BiocGenerics, Biostrings, GenomicRanges, graphics, IRanges, S4Vectors, stringr |
| System Requirements | |
| URL | https://github.com/crisprVerse/crisprBase |
| Bug Reports | https://github.com/crisprVerse/crisprBase/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | crisprDesign, crisprViz |
| Imports Me | crisprBowtie, crisprBwa, crisprShiny, crisprVerse |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | crisprBase_1.8.0.tar.gz |
| Windows Binary (x86_64) | crisprBase_1.8.0.zip |
| macOS Binary (x86_64) | crisprBase_1.8.0.tgz |
| macOS Binary (arm64) | crisprBase_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/crisprBase |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/crisprBase |
| Bioc Package Browser | https://code.bioconductor.org/browse/crisprBase/ |
| Package Short Url | https://bioconductor.org/packages/crisprBase/ |
| Package Downloads Report | Download Stats |