To install this package, start R and enter:

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

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

SGSeq

   

Splice event prediction and quantification from RNA-seq data

Bioconductor version: 3.2

Predict splice junctions and exons from BAM files and obtain compatible read counts and FPKMs. Identify splice events and estimate relative usage of splice variants based on compatible read counts at event boundaries.

Author: Leonard Goldstein

Maintainer: Leonard Goldstein <goldstel at gene.com>

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

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("SGSeq")

 

HTML Splice event prediction and quantification from RNA-seq data
PDF   Reference Manual
Text   NEWS

Details

biocViews AlternativeSplicing, RNASeq, Software, Transcription
Version 1.4.3
In Bioconductor since BioC 3.0 (R-3.1) (1.5 years)
License Artistic-2.0
Depends methods, IRanges, GenomicRanges
Imports AnnotationDbi, BiocGenerics, Biostrings, GenomicAlignments, GenomicFeatures, GenomeInfoDb, igraph, parallel, Rsamtools, rtracklayer, RUnit, S4Vectors, SummarizedExperiment(>= 0.2.0)
LinkingTo
Suggests BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg19.knownGene
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 SGSeq_1.4.3.tar.gz
Windows Binary SGSeq_1.4.3.zip
Mac OS X 10.6 (Snow Leopard) SGSeq_1.4.0.tgz
Mac OS X 10.9 (Mavericks) SGSeq_1.4.3.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/SGSeq/tree/release-3.2
Package Short Url http://bioconductor.org/packages/SGSeq/
Package Downloads Report Download Stats

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