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Mulder2012
Predicting functional networks and modules of chromatin factors controlling adult stem cell fate from RNA interference screens
Bioconductor version: 3.0
This package provides functions to reproduce results and figures in Mulder K. et. al. published in Nature Cell Biology 2012 and Wang X. et. al. published in PLoS Computational Biology 2012.
Author: Xin Wang <Xin.Wang at cancer.org.uk>, Florian Markowetz <Florian.Markowetz at cancer.org.uk>
Maintainer: Xin Wang <Xin.Wang at cancer.org.uk>
Citation (from within R,
enter citation("Mulder2012")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("Mulder2012")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("Mulder2012")
| R Script | Main vignette:Posterior association network and enriched functional gene modules inferred from rich phenotypes of gene perturbations | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Bioinformatics, ExperimentData |
| Version | 0.5.1 |
| License | Artistic-2.0 |
| Depends | R (>= 2.14), org.Hs.eg.db, KEGG.db |
| Imports | igraph, HTSanalyzeR, PANR, RedeR, pvclust, MASS |
| LinkingTo | |
| Suggests | snow |
| 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 | Mulder2012_0.5.1.tar.gz |
| Windows Binary | Mulder2012_0.5.1.zip |
| Mac OS X 10.6 (Snow Leopard) | Mulder2012_0.5.1.tgz |
| Mac OS X 10.9 (Mavericks) | Mulder2012_0.5.1.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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