GUIDEseq specifications

Information


Unique identifier OMICS_18333
Name GUIDEseq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A sequence.
Input format BAM, UMI
Output data A prediction score for each sequence.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.10.0
Stability Stable
Requirements
limma, parallel, BiocGenerics, GenomicRanges, Rsamtools, GenomeInfoDb, Biostrings, BiocStyle, BiocParallel, BSgenome, BSgenome.Hsapiens.UCSC.hg19, RUnit, ChIPpeakAnno, data.table, knitr, matrixStats, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, R(>=3.2.0), hash, CRISPRseek, IRanges(>=2.5.5), S4Vectors(>=0.9.6), GenomicAlignments(>=1.7.3)
Maintained Yes

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Documentation


Maintainer


  • person_outline Lihua Julie Zhu <>

Publication for GUIDEseq

GUIDEseq in publications

 (5)
PMCID: 5918688
PMID: 28931002
DOI: 10.1038/nature24268

[…] guide-seq tag integration efficiencies. to perform guide-seq, sample libraries were assembled as previously described and sequenced on an illumina miseq machine. data was analyzed using open-source guideseq software (version 1.1). guide-seq data can be found in , and are deposited with the ncbi sequence read archive. potential alternate alignments shown in , resulting from rna or dna bulges, […]

PMCID: 5437291
PMID: 28497783
DOI: 10.1038/ncomms15058

[…] proteins such as p53-binding protein 1 or the phosphorylated variant histone h2a.x (γh2a.x) does not label dsbs directly and is unable to identify dna breakpoints with single-nucleotide resolution. guideseq, idlv-mediated dna break capture and high-throughput, genome-wide, translocation sequencing detect dsbs by quantifying the products of non-homologous end-joining repair, potentially missing […]

PMCID: 4980201
PMID: 27347757
DOI: 10.1038/nbt.3620

[…] high-throughput sequencing libraries generated after tag-specific amplification were sequenced using an illumina miseq sequencer as previously described. data was analyzed using open-source guideseq software with a window size of 75 bp and allowing for up to 7 mismatches relative to the intended target site. the threshold of 7 mismatches was chosen as the value where less than 0.001% […]

PMCID: 4851738
PMID: 26735016
DOI: 10.1038/nature16526

[…] prior to high-throughput sequencing on an illumina miseq instrument. guide-seq data was analyzed as previously described using open-source guide-seq analysis software (http://www.jounglab.org/guideseq) and the summarized results can be found in . genomic sites were excluded from analysis on the basis of overlap with background genomic breakpoint regions detected in any of four oligo-only […]

PMCID: 4661947
PMID: 26612492
DOI: 10.1186/s13059-015-0823-x

[…] chromatin state across cell types is not currently feasible., further insight into ot effects has been obtained from direct measurement of indel rates by whole-genome sequencing [], digenome-seq [], guideseq [] and high-throughput genome-wide translocation sequencing (htgts) [], revealing additional complexities associated with crispr specificity [–]. the guide-seq approach suggests wide […]


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GUIDEseq institution(s)
Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA; Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA; Genentech, San Francisco, CA, USA; Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
GUIDEseq funding source(s)
Supported by NIH grant R01AI117839 & R01HL093766.

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