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
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This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see SGSeq.
Splice event prediction and quantification from RNA-seq data
Bioconductor version: 3.3
SGSeq is a software package for analyzing splice events from RNA-seq data. Input data are sequence reads mapped to a reference genome in BAM format. Genes are represented as a genome-wide splice graph, which can be obtained from existing annotation or can be predicted from the data. 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 package includes functions for splice event prediction, quantification, visualization and interpretation.
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
| HTML | R Script | SGSeq |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | AlternativeSplicing, RNASeq, Software, Transcription |
| Version | 1.6.12 |
| In Bioconductor since | BioC 3.0 (R-3.1) (2 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, stats |
| LinkingTo | |
| Suggests | BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown |
| 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_1.6.12.tar.gz |
| Windows Binary | SGSeq_1.6.12.zip |
| Mac OS X 10.9 (Mavericks) | SGSeq_1.6.12.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/SGSeq/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/SGSeq/ |
| Package Downloads Report | Download Stats |
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