CRISPRseek

DOI: 10.18129/B9.bioc.CRISPRseek    

Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems

Bioconductor version: Release (3.6)

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. If GeneRfold and GeneR are installed (http://bioconductor.case.edu/bioconductor/2.8/bioc/html/GeneRfold.html, http://bioc.ism.ac.jp/packages/2.8/bioc/html/GeneR.html), then the minimum free energy and bracket notation of secondary structure of gRNA and gRNA backbone constant region will be included in the summary file. This package leverages Biostrings and BSgenome packages.

Author: Lihua Julie Zhu, Benjamin R. Holmes, Herve Pages, Michael Lawrence, Isana Veksler-Lublinsky, Victor Ambros, Neil Aronin and Michael Brodsky

Maintainer: Lihua Julie Zhu <julie.zhu at umassmed.edu>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CRISPRseek")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CRISPRseek")

 

PDF	R Script	CRISPRseek Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	CRISPR, GeneRegulation, SequenceMatching, Software
Version	1.18.0
In Bioconductor since	BioC 2.14 (R-3.1) (4 years)
License	GPL (>= 2)
Depends	R (>= 3.0.1), BiocGenerics, Biostrings
Imports	parallel, data.table, seqinr, S4Vectors(>= 0.9.25), IRanges, BSgenome, BiocParallel, hash
LinkingTo
Suggests	RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
SystemRequirements
Enhances
URL
Depends On Me	crisprseekplus
Imports Me	GUIDEseq
Suggests Me
Build Report

Package Archives

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

Source Package	CRISPRseek_1.18.0.tar.gz
Windows Binary	CRISPRseek_1.18.0.zip
Mac OS X 10.11 (El Capitan)	CRISPRseek_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CRISPRseek
Package Short Url	http://bioconductor.org/packages/CRISPRseek/
Package Downloads Report	Download Stats