SplicingGraphs
This package is for version 3.10 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: 3.10
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. Pagès
Maintainer: H. Pagès <hpages at fredhutch.org>
citation("SplicingGraphs")
):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SplicingGraphs")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SplicingGraphs")
Splicing graphs and RNA-seq data | R Script | |
Reference Manual |
Details
biocViews | AlternativeSplicing, Annotation, DataRepresentation, GeneExpression, Genetics, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Visualization |
Version | 1.26.1 |
In Bioconductor since | BioC 2.12 (R-3.0) (11 years) |
License | Artistic-2.0 |
Depends | GenomicFeatures(>= 1.17.13), GenomicAlignments(>= 1.1.22), Rgraphviz(>= 2.3.7) |
Imports | methods, utils, graphics, igraph, BiocGenerics, S4Vectors(>= 0.17.5), BiocParallel, IRanges(>= 2.20.1), GenomeInfoDb, GenomicRanges(>= 1.23.21), GenomicFeatures, Rsamtools, GenomicAlignments, graph, Rgraphviz |
System Requirements | |
URL |
See More
Suggests | igraph, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | SplicingGraphs_1.26.1.tar.gz |
Windows Binary | SplicingGraphs_1.26.1.zip |
Mac OS X 10.11 (El Capitan) | SplicingGraphs_1.26.1.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/SplicingGraphs |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SplicingGraphs |
Bioc Package Browser | https://code.bioconductor.org/browse/SplicingGraphs/ |
Package Short Url | https://bioconductor.org/packages/SplicingGraphs/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.10 | Source Archive |