This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see CRISPRseek.
Bioconductor version: 3.13
The package includes functions to find potential guide RNAs for the CRISPR editing system including Base Editors and the Prime Editor 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. The package also output indels and their frequencies for Cas9 targeted sites.
Author: Lihua Julie Zhu, Benjamin R. Holmes, Hervé Pagès, Hui Mao, 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")
):
To install this package, start R (version "4.1") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("CRISPRseek")
For older versions of R, please refer to the appropriate Bioconductor release.
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 |
biocViews | CRISPR, GeneRegulation, ImmunoOncology, SequenceMatching, Software |
Version | 1.32.0 |
In Bioconductor since | BioC 2.14 (R-3.1) (7.5 years) |
License | GPL (>= 2) |
Depends | R (>= 3.0.1), BiocGenerics, Biostrings |
Imports | parallel, data.table, seqinr, S4Vectors(>= 0.9.25), IRanges, BSgenome, BiocParallel, hash, methods, reticulate, rhdf5 |
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, multicrispr |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | CRISPRseek_1.32.0.tar.gz |
Windows Binary | CRISPRseek_1.32.0.zip |
macOS 10.13 (High Sierra) | CRISPRseek_1.32.0.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 |
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