acde: Artificial Components Detection of Differentially Expressed Genes

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This package provides a multivariate inferential analysis method for detecting differentially expressed genes in gene expression data. It uses artificial components, close to the data's principal components but with an exact interpretation in terms of differential genetic expression, to identify differentially expressed genes while controlling the false discovery rate (FDR). The methods on this package are described in the vignette or in the article 'Multivariate Method for Inferential Identification of Differentially Expressed Genes in Gene Expression Experiments' by J. P. Acosta, L. Lopez-Kleine and S. Restrepo (2015, pending publication).

Author
Juan Pablo Acosta, Liliana Lopez-Kleine
Date of publication
None
Maintainer
Juan Pablo Acosta <jpacostar@unal.edu.co>
License
GPL-3
Version
1.4.0

View on Bioconductor

Man pages

ac
Artificial Components for Gene Expression Data
acde-package
Artificial Components Detection of Differentially Expressed...
bcaFDR
BCa Confidence Upper Bound for the FDR
fdr
False Discovery Rate Computation
phytophthora
Gene Expression Data for Tomato Plants Inoculated with...
plot.STP
Plot Method for Single Time Point Analysis
plot.TC
Plot Method for Time Course Analysis
print.STP
Print Method for Single Time Point Analysis
print.TC
Print Method for Time Course Analysis
qval
Q-Values Computation
stp
Single Time Point Analysis for Detecting Differentially...
tc
Time Course Analysis for Detecting Differentially Expressed...

Files in this package

acde/DESCRIPTION
acde/NAMESPACE
acde/NEWS
acde/R
acde/R/ac.R
acde/R/ac2.R
acde/R/bcaFDR.R
acde/R/fdr.R
acde/R/plot.STP.R
acde/R/plot.TC.R
acde/R/print.STP.R
acde/R/print.TC.R
acde/R/qval.R
acde/R/stp.R
acde/R/summary.TC.R
acde/R/tc.R
acde/build
acde/build/vignette.rds
acde/data
acde/data/datalist
acde/data/phytophthora.rda
acde/inst
acde/inst/CITATION
acde/inst/doc
acde/inst/doc/acde.R
acde/inst/doc/acde.Rnw
acde/inst/doc/acde.pdf
acde/inst/unitTests
acde/inst/unitTests/test_acde.R
acde/man
acde/man/ac.Rd
acde/man/acde-package.Rd
acde/man/bcaFDR.Rd
acde/man/fdr.Rd
acde/man/phytophthora.Rd
acde/man/plot.STP.Rd
acde/man/plot.TC.Rd
acde/man/print.STP.Rd
acde/man/print.TC.Rd
acde/man/qval.Rd
acde/man/stp.Rd
acde/man/tc.Rd
acde/tests
acde/tests/runTests.R
acde/vignettes
acde/vignettes/Plot_PI_7.pdf
acde/vignettes/acde.Rnw
acde/vignettes/acde.bib
acde/vignettes/resVignette.rda