To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("EDDA")

In most cases, you don't need to download the package archive at all.

EDDA

Experimental Design in Differential Abundance analysis

Bioconductor version: Release (3.0)

EDDA is a tool for systematic assessment of the impact of experimental design and the statistical test used on the ability to detect differential abundance. EDDA can aid in the design of a range of common experiments such as RNA-seq, ChIP-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. More details of EDDA can be found at Luo, Huaien et al. "The Importance of Study Design for Detecting Differentially Abundant Features in High-Throughput Experiments." Genome Biology 2014;15(12):527 (http://www.ncbi.nlm.nih.gov/pubmed/25517037/). An accompanying web server (http://edda.gis.a-star.edu.sg/) is available for easy access to some functionality of EDDA.

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>

Citation (from within R, enter citation("EDDA")):

Installation

To install this package, start R and enter:

source("http://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 R Script EDDA Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews ChIPSeq, ExperimentalDesign, Normalization, RNASeq, Sequencing, Software
Version 1.5.3
In Bioconductor since BioC 2.14 (R-3.1)
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
Suggests
SystemRequirements
URL http://csb5.github.io/EDDA/
Depends On Me
Imports Me
Suggests Me

Package Archives

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

Package Source EDDA_1.5.3.tar.gz
Windows Binary EDDA_1.5.3.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) EDDA_1.5.3.tgz
Mac OS X 10.9 (Mavericks) EDDA_1.5.3.tgz
Browse/checkout source (username/password: readonly)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center