SplicingGraphs
This package is for version 3.11 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: 3.11
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 "4.0") 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 | 1.28.0 |
| 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(>= 2.21.2), 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_1.28.0.tar.gz |
| Windows Binary | SplicingGraphs_1.28.0.zip |
| macOS 10.13 (High Sierra) | SplicingGraphs_1.28.0.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 3.11 | Source Archive |