SGSeq

DOI: 10.18129/B9.bioc.SGSeq    

Splice event prediction and quantification from RNA-seq data

Bioconductor version: Release (3.6)

SGSeq is a software package for analyzing splice events from RNA-seq data. Input data are RNA-seq reads mapped to a reference genome in BAM format. Genes are represented as a splice graph, which can be obtained from existing annotation or predicted from the mapped sequence reads. Splice events are identified from the graph and are quantified locally using structurally compatible reads at the start or end of each splice variant. The software includes functions for splice event prediction, quantification, visualization and interpretation.

Author: Leonard Goldstein

Maintainer: Leonard Goldstein <goldstel at gene.com>

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

HTML	R Script	SGSeq
PDF		Reference Manual
Text		NEWS

Details

biocViews	AlternativeSplicing, RNASeq, Software, Transcription
Version	1.12.0
In Bioconductor since	BioC 3.0 (R-3.1) (3.5 years)
License	Artistic-2.0
Depends	IRanges, GenomicRanges(>= 1.23.21), Rsamtools, SummarizedExperiment, methods
Imports	AnnotationDbi, BiocGenerics, Biostrings, GenomicAlignments, GenomicFeatures, GenomeInfoDb, RUnit, S4Vectors(>= 0.9.39), grDevices, graphics, igraph, parallel, rtracklayer(>= 1.37.2), stats
LinkingTo
Suggests	BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me	EventPointer
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package	SGSeq_1.12.0.tar.gz
Windows Binary	SGSeq_1.12.0.zip
Mac OS X 10.11 (El Capitan)	SGSeq_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SGSeq
Package Short Url	http://bioconductor.org/packages/SGSeq/
Package Downloads Report	Download Stats