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

 

   

GUIDE-seq analysis pipeline

Bioconductor version: Release (3.5)

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, Herve Pages, 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 R Script GUIDEseq Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews CRISPR, GeneRegulation, Sequencing, Software, WorkflowStep
Version 1.6.1
In Bioconductor since BioC 3.2 (R-3.2) (1.5 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
LinkingTo
Suggests knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
SystemRequirements
Enhances
URL
Depends On Me
Imports Me crisprseekplus
Suggests Me
Build Report  

Package Archives

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

Package Source GUIDEseq_1.6.1.tar.gz
Windows Binary GUIDEseq_1.6.1.zip
Mac OS X 10.11 (El Capitan) GUIDEseq_1.6.1.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/GUIDEseq/tree/release-3.5
Package Short Url http://bioconductor.org/packages/GUIDEseq/
Package Downloads Report Download Stats

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