EDDA

DOI: 10.18129/B9.bioc.EDDA    

Experimental Design in Differential Abundance analysis

Bioconductor version: Release (3.6)

EDDA can aid in the design of a range of common experiments such as RNA-seq, Nanostring assays, RIP-seq and Metagenomic sequencing, and enables researchers to comprehensively investigate the impact of experimental decisions on the ability to detect differential abundance. This work was published on 3 December 2014 at Genome Biology under the title "The importance of study design for detecting differentially abundant features in high-throughput experiments" (http://genomebiology.com/2014/15/12/527).

Author: Li Juntao, Luo Huaien, Chia Kuan Hui Burton, Niranjan Nagarajan

Maintainer: Chia Kuan Hui Burton <chiakhb at gis.a-star.edu.sg>, Niranjan Nagarajan <nagarajann at gis.a-star.edu.sg>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("EDDA")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("EDDA")

 

PDF		EDDA Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	ChIPSeq, ExperimentalDesign, Normalization, RNASeq, Sequencing, Software
Version	1.16.0
In Bioconductor since	BioC 2.14 (R-3.1) (4 years)
License	GPL (>= 2)
Depends	Rcpp (>= 0.10.4), parallel, methods, ROCR, DESeq, baySeq, snow, edgeR
Imports	graphics, stats, utils, parallel, methods, ROCR, DESeq, baySeq, snow, edgeR
LinkingTo	Rcpp
Suggests
SystemRequirements
Enhances
URL	http://edda.gis.a-star.edu.sg/ http://genomebiology.com/2014/15/12/527
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	EDDA_1.16.0.tar.gz
Windows Binary	EDDA_1.16.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	EDDA_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/EDDA
Package Short Url	http://bioconductor.org/packages/EDDA/
Package Downloads Report	Download Stats