GrammR: Graphical Representation and Modeling of Metagenomic Reads

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Represents metagenomic samples on the Euclidean space to examine similarity amongst samples by studying clusters in the model. Given the matrix of metagenomic counts for samples, this package (1) quantifies dissimilarity between samples using Kendall's tau-distance, (2) constructs multidimensional models of different dimension, and (3) plots the models for visualization and comparison.

Author
Deepak Nag Ayyala [aut, cre], Shili Lin [aut]
Date of publication
2016-02-14 17:56:46
Maintainer
Deepak Nag Ayyala <deepaknagayyala@gmail.com>
License
LGPL-3
Version
1.1.0
URLs

View on CRAN

Man pages

Count2Distance
Calculating the dissimilarity matrix for metagenomic count...
GrammRGUI
GrammR GUI for graphical modeling and visualization
GrammR-package
Graphical Representation and Modeling of Metagenomic Reads
GrammRServ
Graphical Representation without a GUI
GraphMetagen
Graphical model construction for metagenomic data
KenDist
Wrapper for the C program which calculates the Kendall's...
MakeGUIPlots
Construct plots for multidimensional scaling models.
MakeServPlots
Construct plots for multidimensional scaling models.
MatrixkNorm
Calculate l_p-norm distance between samples
MCError
Misclassification Error
metagencounts
Randomly generated Metagenomic Counts
OptimClusts
Optimal Cluster Calculator
Summarize
Display summary of the graphical model constructed.

Files in this package

GrammR
GrammR/src
GrammR/src/KendallDistance.c
GrammR/NAMESPACE
GrammR/data
GrammR/data/metagencounts.rda
GrammR/R
GrammR/R/GraphMetagen.R
GrammR/R/Make2DPlots.R
GrammR/R/MakePlots4D.R
GrammR/R/KenDist.R
GrammR/R/Summarize.R
GrammR/R/GrammRServ.R
GrammR/R/MakePlots2D.R
GrammR/R/MCError.R
GrammR/R/MakePlots3D.R
GrammR/R/Make3DPlots.R
GrammR/R/MatrixkNorm.R
GrammR/R/GrammRGUI.R
GrammR/R/OptimClusts.R
GrammR/R/Make4DPlots.R
GrammR/R/Count2Distance.R
GrammR/MD5
GrammR/DESCRIPTION
GrammR/man
GrammR/man/Summarize.Rd
GrammR/man/GraphMetagen.Rd
GrammR/man/OptimClusts.Rd
GrammR/man/metagencounts.Rd
GrammR/man/MakeServPlots.Rd
GrammR/man/GrammRServ.Rd
GrammR/man/MakeGUIPlots.Rd
GrammR/man/Count2Distance.Rd
GrammR/man/GrammRGUI.Rd
GrammR/man/MatrixkNorm.Rd
GrammR/man/GrammR-package.Rd
GrammR/man/KenDist.Rd
GrammR/man/MCError.Rd