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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("rBiopaxParser")
In most cases, you don't need to download the package archive at all.
rBiopaxParser
Parses BioPax files and represents them in R
Bioconductor version: 3.0
Parses BioPAX files and represents them in R, at the moment BioPAX level 2 and level 3 are supported.
Author: Frank Kramer
Maintainer: Frank Kramer <dev at frankkramer.de>
Citation (from within R,
enter citation("rBiopaxParser")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("rBiopaxParser")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("rBiopaxParser")
| R Script | rBiopaxParser Vignette | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataRepresentation, Software |
| Version | 2.4.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) |
| License | GPL (>= 2) |
| Depends | R (>= 3.0.0), data.table |
| Imports | XML |
| LinkingTo | |
| Suggests | Rgraphviz, RCurl, graph, RUnit, BiocGenerics, nem, RBGL |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/frankkramer/rBiopaxParser |
| Depends On Me | |
| Imports Me | |
| Suggests Me | NetPathMiner |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | rBiopaxParser_2.4.0.tar.gz |
| Windows Binary | rBiopaxParser_2.4.0.zip |
| Mac OS X 10.6 (Snow Leopard) | rBiopaxParser_2.4.0.tgz |
| Mac OS X 10.9 (Mavericks) | rBiopaxParser_2.4.0.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
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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