To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("DEDS")
In most cases, you don't need to download the package archive at all.
DEDS
Differential Expression via Distance Summary for Microarray Data
Bioconductor version: 3.0
This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements a new methodology called DEDS (Differential Expression via Distance Summary), which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach.
Author: Yuanyuan Xiao <yxiao at itsa.ucsf.edu>, Jean Yee Hwa Yang <jeany at maths.usyd.edu.au>.
Maintainer: Yuanyuan Xiao <yxiao at itsa.ucsf.edu>
Citation (from within R,
enter citation("DEDS")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("DEDS")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DEDS")
| R Script | DEDS.pdf | |
| Reference Manual |
Details
| biocViews | DifferentialExpression, Microarray, Software |
| Version | 1.40.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier |
| License | LGPL |
| Depends | R (>= 1.7.0) |
| Imports | |
| LinkingTo | |
| Suggests | |
| 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 | DEDS_1.40.0.tar.gz |
| Windows Binary | DEDS_1.40.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | DEDS_1.40.0.tgz |
| Mac OS X 10.9 (Mavericks) | DEDS_1.40.0.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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