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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: 3.0
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. This package leverages Biostrings and BSgenome packages.
Author: Lihua Julie Zhu, Benjamin R. Holmes, Herve Pages, 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")
| R Script | CRISPRseek Vignette | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GeneRegulation, SequenceMatching, Software |
| Version | 1.4.2 |
| In Bioconductor since | BioC 2.14 (R-3.1) |
| 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_1.4.2.tar.gz |
| Windows Binary | CRISPRseek_1.4.2.zip |
| Mac OS X 10.6 (Snow Leopard) | CRISPRseek_1.4.2.tgz |
| Mac OS X 10.9 (Mavericks) | CRISPRseek_1.4.2.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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