To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("XDE")
In most cases, you don't need to download the package archive at all.
XDE
XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression
Bioconductor version: 3.0
Multi-level model for cross-study detection of differential gene expression.
Author: R.B. Scharpf, G. Parmigiani, A.B. Nobel, and H. Tjelmeland
Maintainer: Robert Scharpf <rscharpf at jhsph.edu>
Citation (from within R,
enter citation("XDE")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("XDE")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("XDE")
| R Script | XDE Vignette | |
| R Script | XdeParameterClass Vignette | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DifferentialExpression, Microarray, Software |
| Version | 2.12.0 |
| In Bioconductor since | BioC 2.2 (R-2.7) |
| License | LGPL-2 |
| Depends | R (>= 2.10.0), Biobase(>= 2.5.5), methods, graphics |
| Imports | Biobase, BiocGenerics, genefilter, graphics, grDevices, gtools, MergeMaid, methods, stats, utils, mvtnorm |
| LinkingTo | |
| Suggests | siggenes, genefilter, MASS, RColorBrewer, GeneMeta, RUnit |
| SystemRequirements | |
| Enhances | coda |
| 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 | XDE_2.12.0.tar.gz |
| Windows Binary | XDE_2.12.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | XDE_2.12.0.tgz |
| Mac OS X 10.9 (Mavericks) | XDE_2.12.0.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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