To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("CRISPRseek")

In most cases, you don't need to download the package archive at all.

CRISPRseek

 

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

Bioconductor version: Release (3.1)

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 is installed, 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, Isana Veksler-Lublinsky, Victor Ambros, Neil Aronin and Michael Brodsky

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

Citation (from within R, enter citation("CRISPRseek")):

Installation

To install this package, start R and enter:

source("http://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 GeneRegulation, SequenceMatching, Software
Version 1.8.0
In Bioconductor since BioC 2.14 (R-3.1) (1 years)
License GPL (>= 2)
Depends R (>= 3.0.1), BiocGenerics, Biostrings, BSgenome, seqinr
Imports
LinkingTo
Suggests RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
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 CRISPRseek_1.8.0.tar.gz
Windows Binary CRISPRseek_1.8.0.zip
Mac OS X 10.6 (Snow Leopard) CRISPRseek_1.8.0.tgz
Mac OS X 10.9 (Mavericks) CRISPRseek_1.8.0.tgz
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