MethPed
This package is for version 3.11 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: 3.11
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")):
Installation
To install this package, start R (version "4.0") 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 |
Details
| biocViews | Classification, DNAMethylation, Epigenetics, ImmunoOncology, Software |
| Version | 1.16.0 |
| 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 |
See More
| 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_1.16.0.tar.gz |
| Windows Binary | MethPed_1.16.0.zip |
| macOS 10.13 (High Sierra) | MethPed_1.16.0.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 3.11 | Source Archive |