MethPed

DOI: 10.18129/B9.bioc.MethPed    

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

Bioconductor version: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML	R Script	MethPed User Guide
PDF		Reference Manual

Details

biocViews	Classification, DNAMethylation, Epigenetics, ImmunoOncology, Software
Version	1.20.0
In Bioconductor since	BioC 3.3 (R-3.3) (5.5 years)
License	GPL-2
Depends	R (>= 3.0.0), Biobase
Imports	randomForest, grDevices, graphics, stats
LinkingTo
Suggests	BiocStyle, knitr, markdown, impute
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	MethPed_1.20.0.tar.gz
Windows Binary	MethPed_1.20.0.zip
macOS 10.13 (High Sierra)	MethPed_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MethPed
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MethPed
Package Short Url	https://bioconductor.org/packages/MethPed/
Package Downloads Report	Download Stats