CRISPRseek
This package is for version 3.6 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: 3.6
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>
citation("CRISPRseek")):
Installation
To install this package, start R (version "3.4") 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, SequenceMatching, Software |
| Version | 1.18.0 |
| 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_1.18.0.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 |
| 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 3.6 | Source Archive |