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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 3.4 of Bioconductor; for the stable, up-to-date release version, see GUIDEseq.
GUIDE-seq analysis pipeline
Bioconductor version: 3.4
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, 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")
| R Script | GUIDEseq Vignette | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | CRISPR, GeneRegulation, Sequencing, Software, WorkflowStep |
| Version | 1.4.1 |
| 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_1.4.1.tar.gz |
| Windows Binary | GUIDEseq_1.4.1.zip |
| Mac OS X 10.9 (Mavericks) | GUIDEseq_1.4.1.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/GUIDEseq/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/GUIDEseq/ |
| Package Downloads Report | Download Stats |
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