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

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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.

Author
Deena M.A. Gendoo <deena.gendoo@utoronto.ca>, Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Date of publication
2016-02-25 00:39:19
Maintainer
Deena M.A. Gendoo <deena.gendoo@utoronto.ca>
License
GPL-3
Version
1.0.5
URLs

View on CRAN

Man pages

GTML_Mouse_Preds
Table of Pre-computed MM2S Predictions for 32 replicates of...
Human_Cho_Expr
Gene Expression data from selected samples of the Human CHO...
MM2S.human
MM2S Prediction of Human Medulloblastoma Samples
MM2S.mouse
MM2S Prediction of Mouse Medulloblastoma Samples
MM2Ssetup
MM2S ssGSEA Training Matrix, MB Sample Group information for...
PCARender
PCA Projections of ssGSEA Rank Matrix for Test Samples Onto...
PredictionsBarplot
Stacked Barplot of MM2S Subtype Predictions for Given Samples
PredictionsDistributionBoxplot
Boxplot of MM2S Subtype Predictions for Given Samples
PredictionsDistributionPie
Heatmap of MM2S Subtype Predictions for Given Samples
PredictionsHeatmap
Heatmap of MM2S Subtype Predictions for Given Samples
WNT_Mouse_Expr
Gene Expression data pertaining to the GMTL mouse mode

Files in this package

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