CRISPRseek

This is the development version of CRISPRseek; for the stable release version, see CRISPRseek.

Design of guide RNAs in CRISPR genome-editing systems

Bioconductor version: Development (3.21)

The package encompasses functions to find potential guide RNAs for the CRISPR-based genome-editing systems including the Base Editors and the Prime Editors when supplied with target sequences as input. Users have the flexibility to filter resulting guide RNAs based on parameters such as the absence of restriction enzyme cut sites or the lack of paired guide RNAs. The package also facilitates genome-wide exploration for off-targets, offering features to score and rank off-targets, retrieve flanking sequences, and indicate whether the hits are located within exon regions. All detected guide RNAs are annotated with the cumulative scores of the top5 and topN off-targets together with the detailed information such as mismatch sites and restrictuion enzyme cut sites. The package also outputs 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 Michael Brodsky Devin M Burris

Maintainer: Lihua Julie Zhu <julie.zhu at umassmed.edu> Kai Hu <kai.hu at umassmed.edu>

Citation (from within R, enter citation("CRISPRseek")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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: guide RNA design and off-target analysis	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CRISPR, GeneRegulation, ImmunoOncology, SequenceMatching, Software
Version	1.47.1
In Bioconductor since	BioC 2.14 (R-3.1) (11 years)
License	file LICENSE
Depends	R (>= 3.5.0), BiocGenerics, Biostrings, GenomicFeatures
Imports	parallel, data.table, seqinr, S4Vectors(>= 0.9.25), IRanges, BSgenome, hash, methods, reticulate, rhdf5, XVector, DelayedArray, GenomeInfoDb, GenomicRanges, dplyr, keras, mltools, gtools, openxlsx, rio, rlang, stringr
System Requirements
URL

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, BSgenome.Hsapiens.UCSC.hg38, BiocFileCache, TxDb.Hsapiens.UCSC.hg38.knownGene, testthat, knitr
Linking To
Enhances
Depends On Me
Imports Me	GUIDEseq, multicrispr
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_1.47.1.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)	CRISPRseek_1.47.1.tgz
macOS Binary (arm64)	CRISPRseek_1.47.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CRISPRseek
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CRISPRseek
Bioc Package Browser	https://code.bioconductor.org/browse/CRISPRseek/
Package Short Url	https://bioconductor.org/packages/CRISPRseek/
Package Downloads Report	Download Stats