EDDA

DOI: 10.18129/B9.bioc.EDDA    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see EDDA.

Experimental Design in Differential Abundance analysis

Bioconductor version: 3.9

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 (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("EDDA")

For older versions of R, please refer to the appropriate Bioconductor release.

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, ImmunoOncology, Normalization, RNASeq, Sequencing, Software
Version	1.22.0
In Bioconductor since	BioC 2.14 (R-3.1) (5.5 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
Links To Me
Build Report

Package Archives

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

Source Package	EDDA_1.22.0.tar.gz
Windows Binary	EDDA_1.22.0.zip
Mac OS X 10.11 (El Capitan)	EDDA_1.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/EDDA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/EDDA
Package Short Url	https://bioconductor.org/packages/EDDA/
Package Downloads Report	Download Stats