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: 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")
| 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) |
| 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 |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!
Contact us: support.bioconductor.org
Hosting provided by Fred Hutchinson Cancer Research Center
Copyright © 2003 - 2015, Bioconductor
