CRISPRseek statistics

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Protocols

CRISPRseek specifications

Information


Unique identifier OMICS_08507
Name CRISPRseek
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.20.0
Stability Stable
Requirements
parallel, BiocGenerics, IRanges, Biostrings, BiocStyle, BiocParallel, BSgenome, BSgenome.Hsapiens.UCSC.hg19, RUnit, S4Vectors(>=0.9.25), data.table, org.Hs.eg.db, seqinr, TxDb.Hsapiens.UCSC.hg19.knownGene, R(>=3.0.1), hash
Maintained Yes

Versioning


No version available

Documentation


Maintainers


  • person_outline Michael H. Brodsky
  • person_outline Lihua Julie Zhu

Publication for CRISPRseek

CRISPRseek citations

 (5)
library_books

Editing out five Serpina1 paralogs to create a mouse model of genetic emphysema

2018
Proc Natl Acad Sci U S A
PMCID: 5856518
PMID: 29453277
DOI: 10.1073/pnas.1713689115

[…] nserved regions within the mouse Serpina1 paralogs. CRISPR/Cas9 target sites present in all isoforms and with low predicted off-target activity were identified using the Bioconductor software package CRISPRseek (). Four CRISPR/Cas9 target sequences were selected that are conserved in each of the mouse Serpina paralogs. […]

library_books

Therapeutic genome editing by combined viral and non viral delivery of CRISPR system components in vivo

2016
Nat Biotechnol
PMCID: 5423356
PMID: 26829318
DOI: 10.1038/nbt.3471

[…] together using ChIPpeakAnno. Regions spanning each peak start and end (± 50 bp) were searched for sequence elements that were complementary to the nuclease target site with NGG, NGA or NAG PAMs using CRISPRseek,. Only peaks that harbor a sequence with less than 7 mismatches to the target site were considered potential off-target sites. These regions are reported in with the number of unique reads […]

call_split

Resources for the design of CRISPR gene editing experiments

2015
Genome Biol
PMCID: 4661947
PMID: 26612492
DOI: 10.1186/s13059-015-0823-x
call_split See protocol

[…] r target site identification. Some tools such as SSFinder [] simply output the complete list of PAM sites, leaving the user to dictate subsequent site selection, whereas others such as E-CRISP [] and CRISPRseek [] offer additional criteria to filter or rank the target sites.Next to the PAM requirement, perhaps the most important consideration for CRISPR modifications is the position of the cut sit […]

library_books

DNA binding domain fusions enhance the targeting range and precision of Cas9

2015
Nat Methods
PMCID: 4679368
PMID: 26480473
DOI: 10.1038/nmeth.3624

[…] r do not contain unique reads for both sense and anti-sense libraries were discarded. The remaining peaks were searched for sequence elements that were complementary to the nuclease target site using CRISPRseek. Only peaks that harbor a sequence with less than 7 mismatches to the target site were considered potential off-target sites. These regions are reported in and the number of reads from the […]

library_books

Precision cancer mouse models through genome editing with CRISPR Cas9

2015
Genome Med
PMCID: 4460969
PMID: 26060510
DOI: 10.1186/s13073-015-0178-7

[…] 1. Predict top-ranking single guide RNAs (sgRNAs) using published tools such as CRISPR Design Tool [], sgRNA Designer [], E-CRISP [], via the Cas-OFFinder [] or CRISPRseek [].2. Clone sgRNA into pX330 vector [] for transient expression or improved lentivectors [] for stable expression.3. Several groups have reported being able to increase genome-editing effic […]

Citations

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CRISPRseek institution(s)
Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
CRISPRseek funding source(s)
Supported by the CHDI Foundation, gifts for Huntington’s Disease research at the University of Massachusetts, by the National Institutes of Health (R01GM084361 R01NS38194) and by a National Science Foundation graduate fellowship.

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