CRISPRseek

This package is for version 3.7 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: 3.7

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, Hervé Pagès, Michael Lawrence, 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 (version "3.5") 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 PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews CRISPR, GeneRegulation, SequenceMatching, Software
Version 1.20.0
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_1.20.0.tar.gz
Windows Binary CRISPRseek_1.20.0.zip
Mac OS X 10.11 (El Capitan) CRISPRseek_1.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CRISPRseek
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CRISPRseek
Package Short Url https://bioconductor.org/packages/CRISPRseek/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive