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GUIDE-seq and PEtag-seq analysis pipeline

Bioconductor version: Release (3.19)

The package implements GUIDE-seq and PEtag-seq analysis workflow including functions for filtering UMI and reads with low coverage, 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 with mismatches and indels.

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")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

GUIDEseq Vignette PDF R Script
Reference Manual PDF


biocViews CRISPR, GeneRegulation, ImmunoOncology, Sequencing, Software, WorkflowStep
Version 1.34.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)
License GPL (>= 2)
Depends R (>= 3.5.0), GenomicRanges, BiocGenerics
Imports Biostrings, pwalign, CRISPRseek, ChIPpeakAnno, data.table, matrixStats, BSgenome, parallel, IRanges(>= 2.5.5), S4Vectors(>= 0.9.6), stringr, multtest, GenomicAlignments(>= 1.7.3), GenomeInfoDb, Rsamtools, hash, limma, dplyr, GenomicFeatures, rio, tidyr, tools, methods, purrr, ggplot2, openxlsx, patchwork, rlang
System Requirements
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Suggests knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, TxDb.Hsapiens.UCSC.hg19.knownGene,, testthat (>= 3.0.0)
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Follow Installation instructions to use this package in your R session.

Source Package GUIDEseq_1.34.0.tar.gz
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macOS Binary (x86_64) GUIDEseq_1.34.0.tgz
macOS Binary (arm64) GUIDEseq_1.34.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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