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 | |
| 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 |
Documentation »
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