MethPed

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see MethPed.

A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes

Bioconductor version: 3.10

Classification of pediatric tumors into biologically defined subtypes is challenging and multifaceted approaches are needed. For this aim, we developed a diagnostic classifier based on DNA methylation profiles. We offer MethPed as an easy-to-use toolbox that allows researchers and clinical diagnosticians to test single samples as well as large cohorts for subclass prediction of pediatric brain tumors. The current version of MethPed can classify the following tumor diagnoses/subgroups: Diffuse Intrinsic Pontine Glioma (DIPG), Ependymoma, Embryonal tumors with multilayered rosettes (ETMR), Glioblastoma (GBM), Medulloblastoma (MB) - Group 3 (MB_Gr3), Group 4 (MB_Gr3), Group WNT (MB_WNT), Group SHH (MB_SHH) and Pilocytic Astrocytoma (PiloAstro).

Author: Mohammad Tanvir Ahamed [aut, trl], Anna Danielsson [aut], Szilárd Nemes [aut, trl], Helena Carén [aut, cre, cph]

Maintainer: Helena Carén <helenacarenlab at gmail.com>

Citation (from within R, enter citation("MethPed")):

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MethPed")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MethPed")

MethPed User Guide	HTML	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, DNAMethylation, Epigenetics, ImmunoOncology, Software
Version	1.14.0
In Bioconductor since	BioC 3.3 (R-3.3) (8 years)
License	GPL-2
Depends	R (>= 3.0.0), Biobase
Imports	randomForest, grDevices, graphics, stats
System Requirements
URL

Suggests	BiocStyle, knitr, markdown, impute
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	MethPed_1.14.0.tar.gz
Windows Binary	MethPed_1.14.0.zip
Mac OS X 10.11 (El Capitan)	MethPed_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MethPed
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MethPed
Bioc Package Browser	https://code.bioconductor.org/browse/MethPed/
Package Short Url	https://bioconductor.org/packages/MethPed/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.10	Source Archive