multiDimBio: Multivariate Analysis and Visualization for Biological Data

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Code to support a systems biology research program from inception through publication. The methods focus on dimension reduction approaches to detect patterns in complex, multivariate experimental data and places an emphasis on informative visualizations. The goal for this project is to create a package that will evolve over time, thereby remaining relevant and reflective of current methods and techniques. As a result, we encourage suggested additions to the package, both methodological and graphical.

Author
Samuel V. Scarpino
Date of publication
2016-06-08 17:14:57
Maintainer
Samuel V. Scarpino <scarpino@utexas.edu>
License
GPL (>= 3.0)
Version
1.0.1

View on CRAN

Man pages

binomPower
Power analysis for estimating the heritability of a binomial...
boxWhisker
A function to create a box and whisker plot by group ID
completeData
Function to impute missing data.
CondA
Treatment condition for animals contained in the data set...
CondB
Stress condition for animals contained in the data set Nuclei
Dyad
Housing dyad for animals contained in the data set Nuclei
FSelect
A Function to perform step-wise discriminant analysis using F...
getP
An internal function for getting empirical p values
Groups
The group ID for animals contained in the data set Nuclei
h2Estimate
Estimates the heritability of a binomial trait
IntPlot
A function to visualize the results of a MANOVA
LandscapePlot
A function to visualize the Functional Landscape of measured...
ldaPlot
A function to visualize the results of a discriminant...
Loadings
A function to visualize trait loadings onto discriminant...
makeCompMat
A function to create a pairwise comparison matrix
MeanCent
A function to scale data to mean 0
multiDimBio-package
Multivariate Analysis and Visualization for Biological Data
Nuclei
Brain activity in 14 brain regions for 71 individuals
partialF
A function to compute partial F statistics
PercentMax
A function to scale data to the percent of the maximum...
PermuteLDA
A function to determine whether two groups are in...
plotBinomPower
A function to plot the results of a binomPower run
Power
A function to estimate the error rate for FSelect and...
PPCA
A function to perform a probabilistic principle component...
Scores
Principle component scores based on the data in Nuclei
simPower
An internal function of binomPower, which actually calculates...

Files in this package

multiDimBio
multiDimBio/inst
multiDimBio/inst/CITATION
multiDimBio/NAMESPACE
multiDimBio/data
multiDimBio/data/CondB.RData
multiDimBio/data/CondA.RData
multiDimBio/data/Nuclei.RData
multiDimBio/data/Groups.RData
multiDimBio/data/Scores.RData
multiDimBio/data/Dyad.RData
multiDimBio/R
multiDimBio/R/Loadings.R
multiDimBio/R/Power.R
multiDimBio/R/multiDimBio-package.R
multiDimBio/R/getP.R
multiDimBio/R/boxWhisker.R
multiDimBio/R/simPower.R
multiDimBio/R/plotBinomPower.R
multiDimBio/R/h2Estimate.R
multiDimBio/R/FSelect.R
multiDimBio/R/MeanCent.R
multiDimBio/R/makeCompMat.R
multiDimBio/R/binomPower.R
multiDimBio/R/PPCA.R
multiDimBio/R/ZTrans.R
multiDimBio/R/ldaPlot.R
multiDimBio/R/partialF.R
multiDimBio/R/LandscapePlot.R
multiDimBio/R/completeData.R
multiDimBio/R/PercentMax.R
multiDimBio/R/PermuteLDA.R
multiDimBio/R/IntPlot.R
multiDimBio/MD5
multiDimBio/DESCRIPTION
multiDimBio/man
multiDimBio/man/CondA.Rd
multiDimBio/man/PercentMax.Rd
multiDimBio/man/makeCompMat.Rd
multiDimBio/man/IntPlot.Rd
multiDimBio/man/Scores.Rd
multiDimBio/man/Power.Rd
multiDimBio/man/getP.Rd
multiDimBio/man/simPower.Rd
multiDimBio/man/boxWhisker.Rd
multiDimBio/man/FSelect.Rd
multiDimBio/man/h2Estimate.Rd
multiDimBio/man/ldaPlot.Rd
multiDimBio/man/PermuteLDA.Rd
multiDimBio/man/Loadings.Rd
multiDimBio/man/Groups.Rd
multiDimBio/man/MeanCent.Rd
multiDimBio/man/PPCA.Rd
multiDimBio/man/partialF.Rd
multiDimBio/man/Nuclei.Rd
multiDimBio/man/CondB.Rd
multiDimBio/man/multiDimBio-package.Rd
multiDimBio/man/ztrans.rd
multiDimBio/man/LandscapePlot.Rd
multiDimBio/man/binomPower.Rd
multiDimBio/man/completeData.Rd
multiDimBio/man/plotBinomPower.Rd
multiDimBio/man/Dyad.Rd