maSigPro: Significant Gene Expression Profile Differences in Time Course Gene Expression Data
Version 1.48.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorAna Conesa <aconesa@cipf.es>, Maria Jose Nueda <mj.nueda@ua.es>
Bioconductor views Differential Expression Microarray RNA-Seq TimeCourse
Date of publicationNone
MaintainerMaria Jose Nueda <mj.nueda@ua.es>
LicenseGPL (>= 2)
Version1.48.0
URL http://bioinfo.cipf.es/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("maSigPro")

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

Functions

NBdata Man page
NBdesign Man page
PlotGroups Man page
PlotProfiles Man page
T.fit Man page
average.rows Man page
data.abiotic Man page
edesign.abiotic Man page
edesignCT Man page
edesignDR Man page
fit Source code
get.siggenes Man page Source code
i.rank Man page
maSigPro Man page
maSigProUsersGuide Man page Source code
make.design.matrix Man page
p.vector Man page Source code
position Man page
reg.coeffs Man page
see.genes Man page
stepback Man page Source code
stepfor Man page
suma2Venn Man page
two.ways.stepback Man page
two.ways.stepfor Man page

Files

DESCRIPTION
NAMESPACE
R
R/PlotGroups.R
R/PlotProfiles.R
R/T.fit.R
R/average.rows.R
R/get.siggenes.R
R/i.rank.R
R/maSigPro.R
R/maSigProUsersGuide.R
R/make.design.matrix.R
R/p.vector.R
R/position.R
R/reg.coeffs.R
R/see.genes.R
R/stepback.R
R/stepfor.R
R/suma2Venn.R
R/two.ways.stepback.R
R/two.ways.stepfor.R
build
build/vignette.rds
data
data/NBdata.rda
data/NBdesign.rda
data/data.abiotic.rda
data/edesign.abiotic.rda
data/edesignCT.rda
data/edesignDR.rda
inst
inst/doc
inst/doc/maSigPro.Rnw
inst/doc/maSigPro.pdf
inst/doc/maSigProUsersGuide.pdf
man
man/NBdata.Rd
man/NBdesign.Rd
man/PlotGroups.Rd
man/PlotProfiles.Rd
man/T.fit.Rd
man/average.rows.Rd
man/data.abiotic.Rd
man/edesign.abiotic.Rd
man/edesignCT.Rd
man/edesignDR.Rd
man/get.siggenes.Rd
man/i.rank.Rd
man/maSigPro.Rd
man/maSigProUsersGuide.Rd
man/make.design.matrix.Rd
man/p.vector.Rd
man/position.Rd
man/reg.coeffs.Rd
man/see.genes.Rd
man/stepback.Rd
man/stepfor.Rd
man/suma2Venn.Rd
man/two.ways.stepback.Rd
man/two.ways.stepfor.Rd
vignettes
vignettes/maSigPro.Rnw
maSigPro documentation built on May 20, 2017, 10:50 p.m.