GUIDEseq

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 umassmed.edu>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GUIDEseq")

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

Documentation

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

browseVignettes("GUIDEseq")
GUIDEseq Vignette PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews CRISPR, GeneRegulation, ImmunoOncology, Sequencing, Software, WorkflowStep
Version 1.34.0
In Bioconductor since BioC 3.2 (R-3.2) (9 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
URL
See More
Suggests knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package GUIDEseq_1.34.0.tar.gz
Windows Binary (x86_64) GUIDEseq_1.34.0.zip (64-bit only)
macOS Binary (x86_64) GUIDEseq_1.34.0.tgz
macOS Binary (arm64) GUIDEseq_1.34.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GUIDEseq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GUIDEseq
Bioc Package Browser https://code.bioconductor.org/browse/GUIDEseq/
Package Short Url https://bioconductor.org/packages/GUIDEseq/
Package Downloads Report Download Stats