To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("rTRM")
In most cases, you don't need to download the package archive at all.
rTRM
Identification of transcriptional regulatory modules from PPI networks
Bioconductor version: 3.0
rTRM identifies transcriptional regulatory modules (TRMs) from protein-protein interaction networks.
Author: Diego Diez
Maintainer: Diego Diez <diego10ruiz at gmail.com>
Citation (from within R,
enter citation("rTRM")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("rTRM")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("rTRM")
| R Script | Introduction to rTRM | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GeneRegulation, GraphAndNetwork, Network, Software, Transcription |
| Version | 1.4.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) |
| License | GPL-3 |
| Depends | R (>= 2.10), igraph (>= 0.7), RSQLite |
| Imports | AnnotationDbi |
| LinkingTo | |
| Suggests | RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt, knitr, Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db, org.Mm.eg.db, ggplot2 |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | rTRMui |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | rTRM_1.4.0.tar.gz |
| Windows Binary | rTRM_1.4.0.zip |
| Mac OS X 10.6 (Snow Leopard) | rTRM_1.4.0.tgz |
| Mac OS X 10.9 (Mavericks) | rTRM_1.4.0.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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