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
|
This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see 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:
## 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")
| R Script | SGSeq | |
| Reference Manual |
Details
| biocViews | AlternativeSplicing, RNASeq, Software, Transcription |
| Version | 1.0.6 |
| In Bioconductor since | BioC 3.0 (R-3.1) (1.5 years) |
| 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 |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/SGSeq/tree/release-3.0 |
| Package Short Url | http://bioconductor.org/packages/SGSeq/ |
| Package Downloads Report | Download Stats |
Documentation »
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