To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("vtpnet")
In most cases, you don't need to download the package archive at all.
vtpnet
variant-transcription factor-phenotype networks
Bioconductor version: 3.0
variant-transcription factor-phenotype networks, inspired by Maurano et al., Science (2012), PMID 22955828
Author: VJ Carey <stvjc at channing.harvard.edu>
Maintainer: VJ Carey <stvjc at channing.harvard.edu>
Citation (from within R,
enter citation("vtpnet")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("vtpnet")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("vtpnet")
| R Script | vtpnet: variant-transcription factor-network tools | |
| Reference Manual |
Details
| biocViews | Network, Software |
| Version | 0.6.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) |
| License | Artistic-2.0 |
| Depends | R (>= 3.0.0), graph, GenomicRanges, gwascat, doParallel, foreach |
| Imports | |
| LinkingTo | |
| Suggests | MotifDb, VariantAnnotation, Rgraphviz |
| 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 | vtpnet_0.6.0.tar.gz |
| Windows Binary | vtpnet_0.6.0.zip |
| Mac OS X 10.6 (Snow Leopard) | vtpnet_0.6.0.tgz |
| Mac OS X 10.9 (Mavericks) | vtpnet_0.6.0.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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