maSigPro: Significant Gene Expression Profile Differences in Time Course Gene Expression Data

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maSigPro is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.

Author
Ana Conesa <aconesa@cipf.es>, Maria Jose Nueda <mj.nueda@ua.es>
Date of publication
None
Maintainer
Maria Jose Nueda <mj.nueda@ua.es>
License
GPL (>= 2)
Version
1.46.0
URLs

View on Bioconductor

Man pages

average.rows
Average rows by match and index
data.abiotic
Gene expression data potato abiotic stress
edesign.abiotic
Experimental design potato abiotic stress
edesignCT
Experimental design with a shared time
edesignDR
Experimental design with different replicates
get.siggenes
Extract significant genes for sets of variables in time...
i.rank
Ranks a vector to index
make.design.matrix
Make a design matrix for regression fit of time series gene...
maSigPro
Wrapping function for identifying significant differential...
maSigProUsersGuide
View maSigPro User's Guide
NBdata
RNA-Seq dataset example
NBdesign
Experimental design for RNA-Seq example
PlotGroups
Function for plotting gene expression profile at different...
PlotProfiles
Function for visualization of gene expression profiles
position
Column position of a variable in a data frame
p.vector
Make regression fit for time series gene expression...
reg.coeffs
Calculate true variables regression coefficients
see.genes
Wrapper function for visualization of gene expression values...
stepback
Fitting a linear model by backward-stepwise regression
stepfor
Fitting a linear model by forward-stepwise regression
suma2Venn
Creates a Venn Diagram from a matrix of characters
T.fit
Makes a stepwise regression fit for time series gene...
two.ways.stepback
Fitting a linear model by backward-stepwise regression
two.ways.stepfor
Fitting a linear model by forward-stepwise regression

Files in this package

maSigPro/DESCRIPTION
maSigPro/NAMESPACE
maSigPro/R
maSigPro/R/PlotGroups.R
maSigPro/R/PlotProfiles.R
maSigPro/R/T.fit.R
maSigPro/R/average.rows.R
maSigPro/R/get.siggenes.R
maSigPro/R/i.rank.R
maSigPro/R/maSigPro.R
maSigPro/R/maSigProUsersGuide.R
maSigPro/R/make.design.matrix.R
maSigPro/R/p.vector.R
maSigPro/R/position.R
maSigPro/R/reg.coeffs.R
maSigPro/R/see.genes.R
maSigPro/R/stepback.R
maSigPro/R/stepfor.R
maSigPro/R/suma2Venn.R
maSigPro/R/two.ways.stepback.R
maSigPro/R/two.ways.stepfor.R
maSigPro/build
maSigPro/build/vignette.rds
maSigPro/data
maSigPro/data/NBdata.rda
maSigPro/data/NBdesign.rda
maSigPro/data/data.abiotic.rda
maSigPro/data/edesign.abiotic.rda
maSigPro/data/edesignCT.rda
maSigPro/data/edesignDR.rda
maSigPro/inst
maSigPro/inst/doc
maSigPro/inst/doc/maSigPro.Rnw
maSigPro/inst/doc/maSigPro.pdf
maSigPro/inst/doc/maSigProUsersGuide.pdf
maSigPro/man
maSigPro/man/NBdata.Rd
maSigPro/man/NBdesign.Rd
maSigPro/man/PlotGroups.Rd
maSigPro/man/PlotProfiles.Rd
maSigPro/man/T.fit.Rd
maSigPro/man/average.rows.Rd
maSigPro/man/data.abiotic.Rd
maSigPro/man/edesign.abiotic.Rd
maSigPro/man/edesignCT.Rd
maSigPro/man/edesignDR.Rd
maSigPro/man/get.siggenes.Rd
maSigPro/man/i.rank.Rd
maSigPro/man/maSigPro.Rd
maSigPro/man/maSigProUsersGuide.Rd
maSigPro/man/make.design.matrix.Rd
maSigPro/man/p.vector.Rd
maSigPro/man/position.Rd
maSigPro/man/reg.coeffs.Rd
maSigPro/man/see.genes.Rd
maSigPro/man/stepback.Rd
maSigPro/man/stepfor.Rd
maSigPro/man/suma2Venn.Rd
maSigPro/man/two.ways.stepback.Rd
maSigPro/man/two.ways.stepfor.Rd
maSigPro/vignettes
maSigPro/vignettes/maSigPro.Rnw