To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GUIDEseq")

In most cases, you don't need to download the package archive at all.

GUIDEseq

   

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see GUIDEseq.

GUIDE-seq analysis pipeline

Bioconductor version: 3.2

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

Author: Lihua Julie Zhu, Michael Lawrence, Ankit Gupta, 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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GUIDEseq")

Documentation

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

browseVignettes("GUIDEseq")

 

PDF GUIDEseq Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneRegulation, Sequencing, Software, WorkflowStep
Version 1.0.4
In Bioconductor since BioC 3.2 (R-3.2) (0.5 years)
License GPL (>= 2)
Depends R (>= 3.2.0), IRanges, BiocGenerics, S4Vectors
Imports BiocParallel, Biostrings, CRISPRseek, ChIPpeakAnno, GenomicRanges, data.table, matrixStats, BSgenome, parallel
LinkingTo
Suggests knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source GUIDEseq_1.0.4.tar.gz
Windows Binary GUIDEseq_1.0.4.zip
Mac OS X 10.6 (Snow Leopard) GUIDEseq_0.99.6.tgz
Mac OS X 10.9 (Mavericks) GUIDEseq_1.0.4.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/GUIDEseq/tree/release-3.2
Package Short Url http://bioconductor.org/packages/GUIDEseq/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Fred Hutchinson Cancer Research Center