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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SplicingGraphs")
In most cases, you don't need to download the package archive at all.
SplicingGraphs
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This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see SplicingGraphs.
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Bioconductor version: 3.3
This package allows the user to create, manipulate, and visualize splicing graphs and their bubbles based on a gene model for a given organism. Additionally it allows the user to assign RNA-seq reads to the edges of a set of splicing graphs, and to summarize them in different ways.
Author: D. Bindreither, M. Carlson, M. Morgan, H. Pages
Maintainer: H. Pages <hpages at fredhutch.org>
Citation (from within R,
enter citation("SplicingGraphs")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SplicingGraphs")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SplicingGraphs")
| R Script | Splicing graphs and RNA-seq data | |
| Reference Manual |
Details
| biocViews | AlternativeSplicing, Annotation, DataRepresentation, GeneExpression, Genetics, RNASeq, Sequencing, Software, Transcription, Visualization |
| Version | 1.12.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (3.5 years) |
| License | Artistic-2.0 |
| Depends | GenomicFeatures(>= 1.17.13), GenomicAlignments(>= 1.1.22), Rgraphviz(>= 2.3.7) |
| Imports | methods, utils, igraph, BiocGenerics, S4Vectors(>= 0.9.25), IRanges(>= 2.3.21), GenomeInfoDb, GenomicRanges(>= 1.23.21), GenomicFeatures, Rsamtools, GenomicAlignments, graph, Rgraphviz |
| LinkingTo | |
| Suggests | igraph, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit |
| 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 | SplicingGraphs_1.12.0.tar.gz |
| Windows Binary | SplicingGraphs_1.12.0.zip |
| Mac OS X 10.9 (Mavericks) | SplicingGraphs_1.12.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/SplicingGraphs/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/SplicingGraphs/ |
| Package Downloads Report | Download Stats |
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