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MethPed

This is the development version of MethPed; for the stable release version, see MethPed.

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


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Classification, DNAMethylation, Epigenetics, ImmunoOncology, Software
Version 1.31.0
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
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Suggests BiocStyle, knitr, markdown, impute
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Package Archives

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

Source Package MethPed_1.31.0.tar.gz
Windows Binary MethPed_1.31.0.zip (64-bit only)
macOS Binary (x86_64) MethPed_1.31.0.tgz
macOS Binary (arm64)
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/
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