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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "CRISPRseek" in publications use:'
type: software
license: GPL-2.0-or-later
title: 'CRISPRseek: Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing
  systems'
version: 1.45.0
identifiers:
- type: doi
  value: 10.32614/CRAN.package.CRISPRseek
abstract: 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.
authors:
- family-names: Zhu
  given-names: Lihua Julie
  email: julie.zhu@umassmed.edu
- family-names: Zhu
  given-names: Lihua Julie
- family-names: Scemama
  given-names: Paul
- family-names: Holmes
  given-names: Benjamin R.
- family-names: Pagès
  given-names: Hervé
- family-names: Hu
  given-names: Kai
- family-names: Mao
  given-names: Hui
- family-names: Lawrence
  given-names: Michael
- family-names: Veksler-Lublinsky
  given-names: Isana
- family-names: Ambros
  given-names: Victor
- family-names: Aronin
  given-names: Neil
- family-names: Brodsky
  given-names: Michael
preferred-citation:
  type: article
  title: 'CRISPRseek: A Bioconductor Package to Identify Target-Specific Guide RNAs
    for CRISPR-Cas9 Genome-Editing Systems'
  authors:
  - family-names: Zhu
    given-names: Lihua Julie
    email: julie.zhu@umassmed.edu
  - family-names: Holmes
    given-names: Benjamin R.
  - family-names: Aronin
    given-names: Neil
  - family-names: Brodsky
    given-names: Michael H.
  journal: PLoS one
  volume: '9'
  year: '2014'
  issue: '9'
  url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4172692/
  abstract: CRISPR-Cas systems are a diverse family of RNA-protein complexes in bacteria
    that target foreign DNA sequences for cleavage. Derivatives of these complexes
    have been engineered to cleave specific target sequences depending on the sequence
    of a CRISPR-derived guide RNA (gRNA) and the source of the Cas9 protein. Important
    considerations for the design of gRNAs are to maximize aimed activity at the desired
    target site while minimizing off-target cleavage. Because of the rapid advances
    in the understanding of existing CRISPR-Cas9-derived RNA-guided nucleases and
    the development of novel RNA-guided nuclease systems, it is critical to have computational
    tools that can accommodate a wide range of different parameters for the design
    of target-specific RNA-guided nuclease systems. We have developed CRISPRseek,
    a highly flexible, open source software package to identify gRNAs that target
    a given input sequence while minimizing off-target cleavage at other sites within
    any selected genome. CRISPRseek will identify potential gRNAs that target a sequence
    of interest for CRISPR-Cas9 systems from different bacterial species and generate
    a cleavage score for potential off-target sequences utilizing published or user-supplied
    weight matrices with position-specific mismatch penalty scores. Identified gRNAs
    may be further filtered to only include those that occur in paired orientations
    for increased specificity and/or those that overlap restriction enzyme sites.
    For applications where gRNAs are desired to discriminate between two related sequences,
    CRISPRseek can rank gRNAs based on the difference between predicted cleavage scores
    in each input sequence. CRISPRseek is implemented as a Bioconductor package within
    the R statistical programming environment, allowing it to be incorporated into
    computational pipelines to automate the design of gRNAs for target sequences identified
    in a wide variety of genome-wide analyses. CRISPRseek is available under the GNU
    General Public Licence v3.0 at http://www.bioconductor.org.
repository: https://bioc.r-universe.dev
commit: d63723fd8a804eb8f5454a433b08d3bb711dc489
date-released: '2022-06-21'
contact:
- family-names: Zhu
  given-names: Lihua Julie
  email: julie.zhu@umassmed.edu
references:
- type: article
  title: Overview of guide RNA design tools for CRISPR-Cas9 genome editing technology
  authors:
  - family-names: Zhu
    given-names: Lihua Julie
  journal: Front. Biol.
  volume: '10'
  year: '2015'
  issue: '4'
  abstract: CRISPR-Cas (Clustered, Regularly Interspaced, Short Palindromic Repeats
    CRISPR-associated (Cas)) RNA guided endonuclease has emerged as the most effective
    and widely used genome editing technology, which has become the most exciting
    and rapidly advancing research field. Efficient genome editing by the CRISPR-Cas9
    system has been demonstrated in many species, and several labs have established
    CRISPR-Cas9 as a screening tool for systematic genetic analysis, similar to shRNA
    screening. At least three companies have been founded to leverage this technology
    for therapeutic uses. To facilitate the implementation of this technology, many
    software tools have been developed to identify guide RNAs that effectively target
    a desired genomic region. Here, I provide an overview of the technology, focusing
    on guide RNA design principles, available software tools and their strengths and
    weaknesses.