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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CRISPRseek")
In most cases, you don't need to download the package archive at all.
CRISPRseek
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Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems
Bioconductor version: Release (3.4)
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 (from within R,
enter citation("CRISPRseek")):
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")
| R Script | CRISPRseek Vignette | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | CRISPR, GeneRegulation, SequenceMatching, Software |
| Version | 1.14.1 |
| In Bioconductor since | BioC 2.14 (R-3.1) (3 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.
| Package Source | CRISPRseek_1.14.1.tar.gz |
| Windows Binary | CRISPRseek_1.14.1.zip |
| Mac OS X 10.9 (Mavericks) | CRISPRseek_1.14.1.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/CRISPRseek/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/CRISPRseek/ |
| Package Downloads Report | Download Stats |
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