CRISPRseek

DOI: 10.18129/B9.bioc.CRISPRseek    

This package is for version 3.15 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: 3.15

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, Paul Scemama, Benjamin R. Holmes, Hervé Pagès, Kai Hu, Hui Mao, Michael Lawrence, Isana Veksler-Lublinsky, Victor Ambros, Neil Aronin and Michael Brodsky

Maintainer: Lihua Julie Zhu <julie.zhu at umassmed.edu>

Installation

To install this package, start R (version "4.2") 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")

 

PDF	R Script	CRISPRseek Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	CRISPR, GeneRegulation, ImmunoOncology, SequenceMatching, Software
Version	1.36.0
In Bioconductor since	BioC 2.14 (R-3.1) (8.5 years)
License	GPL (>= 2)
Depends	R (>= 3.5.0), BiocGenerics, Biostrings
Imports	parallel, data.table, seqinr, S4Vectors(>= 0.9.25), IRanges, BSgenome, hash, methods, reticulate, rhdf5, XVector, DelayedArray, GenomeInfoDb, GenomicRanges, dplyr, keras, mltools
LinkingTo
Suggests	RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, lattice, MASS, tensorflow, testthat
SystemRequirements
Enhances
URL
Depends On Me	crisprseekplus
Imports Me	GUIDEseq, multicrispr
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	CRISPRseek_1.36.0.tar.gz
Windows Binary	CRISPRseek_1.36.0.zip
macOS Binary (x86_64)	CRISPRseek_1.35.3.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