To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("SGSeq")

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

SGSeq

Prediction, quantification and visualization of alternative transcript events from RNA-seq data

Bioconductor version: 3.0

RNA-seq data are informative for the analysis of known and novel transcript isoforms. While the short length of RNA-seq reads limits the ability to predict and quantify full-length transcripts, short read data are well suited for the analysis of individual alternative transcripts events (e.g. inclusion or skipping of a cassette exon). The SGSeq package enables the prediction, quantification and visualization of alternative transcript events from BAM files.

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:

source("http://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")

 

PDF R Script SGSeq
PDF   Reference Manual

Details

biocViews AlternativeSplicing, RNASeq, Software, Transcription
Version 1.0.6
In Bioconductor since BioC 3.0 (R-3.1)
License Artistic-2.0
Depends BiocParallel, GenomicRanges, IRanges, methods
Imports AnnotationDbi, BiocGenerics, Biostrings, GenomicAlignments, GenomicFeatures, GenomeInfoDb, igraph, parallel, Rsamtools, rtracklayer, S4Vectors(>= 0.2.3)
LinkingTo
Suggests BiocStyle, knitr, 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_1.0.6.tar.gz
Windows Binary SGSeq_1.0.6.zip
Mac OS X 10.6 (Snow Leopard) SGSeq_1.0.6.tgz
Mac OS X 10.9 (Mavericks) SGSeq_1.0.6.tgz
Browse/checkout source (username/password: readonly)
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