MM2S: Single-Sample Classifier of Medulloblastoma Subtypes for Medulloblastoma Patient Samples, Mouse Models, and Cell Lines

Description: A single-sample classifier that generates Medulloblastoma (MB) subtype predictions for single-samples of human MB patients and model systems, including cell lines and mouse-models. The MM2S algorithm uses a systems-based methodology that facilitates application of the algorithm on samples irrespective of their platform or source of origin. MM2S demonstrates > 96% accuracy for patients of well-characterized normal cerebellum, Wingless (WNT), or Sonic hedgehog (SHH) subtypes, and the less-characterized Group4 (86%) and Group3 (78.2%). MM2S also enables classification of MB cell lines and mouse models into their human counterparts.This package contains function for implementing the classifier onto human data and mouse data, as well as graphical rendering of the results as PCA plots and heatmaps.

Install the latest version of this package by entering the following in R:
install.packages("MM2S")
AuthorDeena M.A. Gendoo <deena.gendoo@utoronto.ca>, Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Bioconductor views Cancer Classification MM2Sdata Microarray Software Visualization
Date of publication2016-02-25 00:39:19
MaintainerDeena M.A. Gendoo <deena.gendoo@utoronto.ca>
LicenseGPL-3
Version1.0.5
http://www.sciencedirect.com/science/article/pii/S0888754315000774, http://www.pmgenomics.ca/bhklab/software/mm2s

View on CRAN

Files

inst
inst/doc
inst/doc/MM2S.Rnw
inst/doc/MM2S_FromRawData.pdf
inst/doc/MM2S_FromRawData.R
inst/doc/MM2S_Vignette_FrozenCapture.pdf
inst/doc/MM2S.pdf
inst/doc/MM2S_FromRawData.Rnw
inst/doc/MM2S_FromRawData_Vignette_FrozenCapture.pdf
inst/doc/MM2S.R
NAMESPACE
NEWS
data
data/MM2Ssetup.rda
data/WNT_Mouse_Expr.rda
data/Human_Cho_Expr.rda
data/datalist
data/GTML_Mouse_Preds.rda
R
R/MM2S.mouse.R R/PredictionsDistributionBoxplot.R R/PredictionsDistributionPie.R R/PCARender.R R/MM2S.human.R R/PredictionsHeatmap.R R/PredictionsBarplot.R
vignettes
vignettes/MM2S.Rnw
vignettes/MM2S_FromRawData.Rnw
MD5
README
build
build/vignette.rds
DESCRIPTION
man
man/MM2Ssetup.Rd man/GTML_Mouse_Preds.Rd man/MM2S.human.Rd man/PredictionsDistributionPie.Rd man/WNT_Mouse_Expr.Rd man/PredictionsDistributionBoxplot.Rd man/PredictionsHeatmap.Rd man/MM2S.mouse.Rd man/Human_Cho_Expr.Rd man/PredictionsBarplot.Rd man/PCARender.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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