EDDA
This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last 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>
citation("EDDA")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("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")| EDDA Vignette | |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | ChIPSeq, ExperimentalDesign, ImmunoOncology, Normalization, RNASeq, Sequencing, Software |
| Version | 1.22.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (10 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 |
| System Requirements | |
| URL | http://edda.gis.a-star.edu.sg/ http://genomebiology.com/2014/15/12/527 |
See More
| Suggests | |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/EDDA/ |
| Package Short Url | https://bioconductor.org/packages/EDDA/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |