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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MethPed")
In most cases, you don't need to download the package archive at all.
MethPed
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A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes
Bioconductor version: Release (3.5)
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MethPed")
Documentation
| HTML | R Script | MethPed User Guide |
| Reference Manual |
Details
| biocViews | Classification, DNAMethylation, Epigenetics, Software |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (1.5 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 | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MethPed_1.4.0.tar.gz |
| Windows Binary | MethPed_1.4.0.zip |
| Mac OS X 10.11 (El Capitan) | MethPed_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MethPed |
| Package Short Url | http://bioconductor.org/packages/MethPed/ |
| Package Downloads Report | Download Stats |
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