EDDA: Experimental Design in Differential Abundance analysis

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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
Date of publication
None
Maintainer
Chia Kuan Hui Burton <chiakhb@gis.a-star.edu.sg>, Niranjan Nagarajan <nagarajann@gis.a-star.edu.sg>
License
GPL (>= 2)
Version
1.12.0
URLs

View on Bioconductor

Man pages

BP
BaySeq Profile used in simulations by Hardcastle et al
computeAUC
compute AUC values.
EDDA-package
Experimental Design in Differential Abundance analysis
generateData
generate count data
HBR
Average abundance for RNA-seq data from Human Brain...
plotPRC
plot precision-recall curves
plotROC
plot Receiver Operating Characteristic curve
SingleCell
Single-cell RNA-seq data for model free simulation
testDATs
Run differential abundance testings
Wu
Average abundance for RNA-seq data from schizophrenia.

Files in this package

EDDA/DESCRIPTION
EDDA/NAMESPACE
EDDA/NEWS
EDDA/R
EDDA/R/Cuffdiff.R
EDDA/R/MODEnormalization.R
EDDA/R/Metastats.R
EDDA/R/NOISeq.R
EDDA/R/computeAUC.R
EDDA/R/computeROC.R
EDDA/R/edgeR.R
EDDA/R/generateData.R
EDDA/R/plotPRC.R
EDDA/R/plotROC.R
EDDA/R/run_Cuffdiff.R
EDDA/R/run_DESeq.R
EDDA/R/run_MetaStats.R
EDDA/R/run_NOISeq.R
EDDA/R/run_baySeq.R
EDDA/R/run_edgeR.R
EDDA/R/testDATs.R
EDDA/README.md
EDDA/build
EDDA/build/vignette.rds
EDDA/data
EDDA/data/BP.txt.gz
EDDA/data/HBR.txt.gz
EDDA/data/SingleCell.txt.gz
EDDA/data/Wu.txt.gz
EDDA/data/datalist
EDDA/inst
EDDA/inst/doc
EDDA/inst/doc/EDDA.Rnw
EDDA/inst/doc/EDDA.pdf
EDDA/man
EDDA/man/BP.Rd
EDDA/man/EDDA-package.Rd
EDDA/man/HBR.Rd
EDDA/man/SingleCell.Rd
EDDA/man/Wu.Rd
EDDA/man/computeAUC.Rd
EDDA/man/generateData.Rd
EDDA/man/plotPRC.Rd
EDDA/man/plotROC.Rd
EDDA/man/testDATs.Rd
EDDA/src
EDDA/src/Makevars
EDDA/src/Makevars.win
EDDA/src/cuffdiff.cpp
EDDA/src/cuffdiff.h
EDDA/vignettes
EDDA/vignettes/EDDA.Rnw