To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("EDDA")
In most cases, you don't need to download the package archive at all.
EDDA
|
This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see EDDA.
Experimental Design in Differential Abundance analysis
Bioconductor version: 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:
## 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")
| R Script | EDDA Vignette | |
| 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) (2 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://csb5.github.io/EDDA/ |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
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 |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/EDDA/tree/release-3.0 |
| Package Short Url | http://bioconductor.org/packages/EDDA/ |
| Package Downloads Report | Download Stats |
Documentation »
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