DOI: 10.18129/B9.bioc.GUIDEseq    

GUIDE-seq analysis pipeline

Bioconductor version: Release (3.6)

The package implements GUIDE-seq analysis workflow including functions for obtaining unique insertion sites (proxy of cleavage sites), estimating the locations of the insertion sites, aka, peaks, merging estimated insertion sites from plus and minus strand, and performing off target search of the extended regions around insertion sites.

Author: Lihua Julie Zhu, Michael Lawrence, Ankit Gupta, Hervé Pagès, Alper Kucukural, Manuel Garber, Scot A. Wolfe

Maintainer: Lihua Julie Zhu <julie.zhu at>

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


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PDF R Script GUIDEseq Vignette
PDF   Reference Manual
Text   NEWS


biocViews CRISPR, GeneRegulation, Sequencing, Software, WorkflowStep
Version 1.8.1
In Bioconductor since BioC 3.2 (R-3.2) (2.5 years)
License GPL (>= 2)
Depends R (>= 3.2.0), GenomicRanges, BiocGenerics
Imports BiocParallel, Biostrings, CRISPRseek, ChIPpeakAnno, data.table, matrixStats, BSgenome, parallel, IRanges(>= 2.5.5), S4Vectors(>= 0.9.6), GenomicAlignments(>= 1.7.3), GenomeInfoDb, Rsamtools, hash, limma
Suggests knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene,
Depends On Me
Imports Me crisprseekplus
Suggests Me
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