GUIDEseq

DOI: 10.18129/B9.bioc.GUIDEseq    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see GUIDEseq.

GUIDE-seq and PEtag-seq analysis pipeline

Bioconductor version: 3.15

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.

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>

Installation

To install this package, start R (version "4.2") 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")

 

PDF	R Script	GUIDEseq Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	CRISPR, GeneRegulation, ImmunoOncology, Sequencing, Software, WorkflowStep
Version	1.26.0
In Bioconductor since	BioC 3.2 (R-3.2) (7 years)
License	GPL (>= 2)
Depends	R (>= 3.5.0), 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, dplyr, GenomicFeatures
LinkingTo
Suggests	knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	crisprseekplus
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	GUIDEseq_1.26.0.tar.gz
Windows Binary	GUIDEseq_1.26.0.zip
macOS Binary (x86_64)	GUIDEseq_1.26.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GUIDEseq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GUIDEseq
Package Short Url	https://bioconductor.org/packages/GUIDEseq/
Package Downloads Report	Download Stats