Significant Gene Expression Profile Differences in Time Course Gene Expression Data

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Documentation for package ‘maSigPro’ version 1.72.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help 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 series gene expression experiments
getDS	Extract lists of significant isoforms from Differentially Spliced Genes (DSG)
getDSPatterns	Lists of genes with Isoforms in different clusters
i.rank	Ranks a vector to index
ISOdata	RNA-Seq dataset example for isoforms
ISOdesign	Experimental design for ISOdata dataset example
IsoModel	Detection of genes with Isoforms with different gene expression in time course experiments
IsoPlot	Plotting the isoform profiles of a specific gene by groups
make.design.matrix	Make a design matrix for regression fit of time series gene expression experiments
maSigProUsersGuide	View maSigPro User's Guide
NBdata	RNA-Seq dataset example
NBdesign	Experimental design for RNA-Seq example
p.vector	Make regression fit for time series gene expression experiments
PlotGroups	Function for plotting gene expression profile at different experimental groups
PlotProfiles	Function for visualization of gene expression profiles
PodiumChange	Detection of Genes with switchs of their major isoforms
position	Column position of a variable in a data frame
reg.coeffs	Calculate true variables regression coefficients
see.genes	Wrapper function for visualization of gene expression values of time course experiments
seeDS	Wrapper function for visualization of significant isoforms from Differentially Spliced Genes
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 expression experiments
tableDS	Identification of Mayor and minor Isoforms in the clusters
two.ways.stepback	Fitting a linear model by backward-stepwise regression
two.ways.stepfor	Fitting a linear model by forward-stepwise regression