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CRISPRseek

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

Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") 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 Vignette PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews CRISPR, GeneRegulation, ImmunoOncology, SequenceMatching, Software
Version 1.43.0
In Bioconductor since BioC 2.14 (R-3.1) (10 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
System Requirements
URL
See More
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
Linking To
Enhances
Depends On Me crisprseekplus
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_1.43.0.tar.gz
Windows Binary CRISPRseek_1.43.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)
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