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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("SplicingGraphs")
In most cases, you don't need to download the package archive at all.
SplicingGraphs
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Bioconductor version: 2.14
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 fhcrc.org>
Citation (from within R,
enter citation("SplicingGraphs")):
Installation
To install this package, start R and enter:
source("http://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 | Annotation, DataRepresentation, GeneExpression, Genetics, RNASeq, Sequencing, Software, Visualization |
| Version | 1.4.1 |
| In Bioconductor since | BioC 2.12 (R-3.0) |
| License | Artistic-2.0 |
| Depends | BiocGenerics, IRanges(>= 1.17.43), GenomicRanges(>= 1.15.12), GenomicFeatures, GenomicAlignments(>= 1.0.3), Rgraphviz(>= 2.3.7) |
| Imports | methods, utils, igraph, BiocGenerics, IRanges, GenomicRanges, GenomicFeatures, GenomicAlignments, graph, Rgraphviz |
| Suggests | igraph, Gviz, Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | SplicingGraphs_1.4.1.tar.gz |
| Windows Binary | SplicingGraphs_1.4.1.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | SplicingGraphs_1.4.1.tgz |
| Mac OS X 10.9 (Mavericks) | SplicingGraphs_1.4.1.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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