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 (3.24)
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("MethPed")):Mohammad Tanvir Ahamed, Anna Danielsson, Szilárd Nemes, Helena Carén. MethPed: A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes. doi:10.18129/B9.bioc.MethPed, R package version 1.41.0, https://bioconductor.org/packages/MethPed.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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__A DNA Methylation Classifier Tool for the Identification of Pediatric Brain Tumor Subtypes | HTML | R Script |
| Reference Manual |
Details
| biocViews | Classification, DNAMethylation, Epigenetics, ImmunoOncology, Software |
| Version | 1.41.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 years) |
| License | GPL-2 |
| Depends | R (>= 3.0.0), Biobase |
| Imports | randomForest, grDevices, graphics, stats |
| System Requirements | |
| URL |
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| Suggests | BiocStyle, knitr, markdown, impute |
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| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MethPed_1.41.0.tar.gz |
| Windows Binary (x86_64) | MethPed_1.41.0.zip |
| macOS Binary (big-sur-x86_64) | MethPed_1.41.0.tgz |
| macOS Binary (sonoma-arm64) | MethPed_1.41.0.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 |