CRISPRseek
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see CRISPRseek.
Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems
Bioconductor version: 3.9
The package includes functions to find potential guide RNAs for input target sequences, optionally filter guide RNAs without restriction enzyme cut site, or without paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank sequence and indicate whether the target and off-targets are located in exon region or not. Potential guide RNAs are annotated with total score of the top5 and topN off-targets, detailed topN mismatch sites, restriction enzyme cut sites, and paired guide RNAs. This package leverages Biostrings and BSgenome packages.
Author: Lihua Julie Zhu, Benjamin R. Holmes, Hervé Pagès, Michael Lawrence, Isana Veksler-Lublinsky, Victor Ambros, Neil Aronin and Michael Brodsky
Maintainer: Lihua Julie Zhu <julie.zhu at umassmed.edu>
citation("CRISPRseek")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CRISPRseek")
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("CRISPRseek")| CRISPRseek Vignette | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CRISPR, GeneRegulation, ImmunoOncology, SequenceMatching, Software |
| Version | 1.24.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (10 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.0.1), BiocGenerics, Biostrings |
| Imports | parallel, data.table, seqinr, S4Vectors(>= 0.9.25), IRanges, BSgenome, BiocParallel, hash |
| System Requirements | |
| URL |
See More
| Suggests | RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db |
| Linking To | |
| Enhances | |
| Depends On Me | crisprseekplus |
| Imports Me | GUIDEseq |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CRISPRseek_1.24.0.tar.gz |
| Windows Binary | CRISPRseek_1.24.0.zip |
| Mac OS X 10.11 (El Capitan) | CRISPRseek_1.24.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CRISPRseek |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CRISPRseek |
| Bioc Package Browser | https://code.bioconductor.org/browse/CRISPRseek/ |
| Package Short Url | https://bioconductor.org/packages/CRISPRseek/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |