splineTCDiffExpr: Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction

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This package provides functions for differential gene expression analysis of gene expression time-course data. Natural cubic spline regression models are used. Identified genes may further be used for pathway enrichment analysis and/or the reconstruction of time dependent gene regulatory association networks.

Author
Agata Michna
Date of publication
None
Maintainer
Herbert Braselmann <braselm@helmholtz-muenchen.de>, Agata Michna <agata.michna@helmholtz-muenchen.de>
License
GPL-3
Version
0.99.4

View on Bioconductor

Man pages

networkProperties
Scale-free properties of a network
pathEnrich
Pathway enrichment analysis
splineDiffExprs
Differential expression analysis based on natural cubic...
splineNetRecon
Network reconstruction based on partial correlation method...
splinePlot
Plot spline regression curves of time-course data
TCsimData
Simulated time-course gene expression data set

Files in this package

splineTCDiffExpr/DESCRIPTION
splineTCDiffExpr/NAMESPACE
splineTCDiffExpr/R
splineTCDiffExpr/R/networkProperties.R
splineTCDiffExpr/R/pathEnrich.R
splineTCDiffExpr/R/splineDiffExprs.R
splineTCDiffExpr/R/splineNetRecon.R
splineTCDiffExpr/R/splinePlot.R
splineTCDiffExpr/build
splineTCDiffExpr/build/vignette.rds
splineTCDiffExpr/data
splineTCDiffExpr/data/TCsimData.rda
splineTCDiffExpr/data/datalist
splineTCDiffExpr/inst
splineTCDiffExpr/inst/doc
splineTCDiffExpr/inst/doc/splineTCDiffExpr.R
splineTCDiffExpr/inst/doc/splineTCDiffExpr.Rnw
splineTCDiffExpr/inst/doc/splineTCDiffExpr.pdf
splineTCDiffExpr/inst/extdata
splineTCDiffExpr/inst/extdata/c2.cp.kegg.v5.0.symbols.gmt
splineTCDiffExpr/man
splineTCDiffExpr/man/TCsimData.Rd
splineTCDiffExpr/man/networkProperties.Rd
splineTCDiffExpr/man/pathEnrich.Rd
splineTCDiffExpr/man/splineDiffExprs.Rd
splineTCDiffExpr/man/splineNetRecon.Rd
splineTCDiffExpr/man/splinePlot.Rd
splineTCDiffExpr/vignettes
splineTCDiffExpr/vignettes/splineTCDiffExpr.Rnw
splineTCDiffExpr/vignettes/splineTCDiffExpr.bib