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

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).

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MethPed")
AuthorMohammad Tanvir Ahamed [aut, trl], Anna Danielsson [aut], Szilárd Nemes [aut, trl], Helena Carén [aut, cre, cph]
Bioconductor views Classification DNAMethylation Epigenetics
Date of publicationNone
MaintainerHelena Carén <helenacarenlab@gmail.com>
LicenseGPL-2
Version1.2.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/MethPed.R R/MethPed_checkNA.R R/MethPed_dataset.R R/MethPed_plot.methped.R R/MethPed_probeMis.R R/MethPed_summary.methped.R
R/sysdata.rda
build
build/vignette.rds
data
data/MethPed_900probes.rda
data/MethPed_sample.rda
data/datalist
inst
inst/doc
inst/doc/MethPed-vignette.R
inst/doc/MethPed-vignette.Rmd
inst/doc/MethPed-vignette.html
man
man/MethPed.Rd man/MethPed_900probes.Rd man/MethPed_sample.Rd man/checkNA.Rd man/plot.methped.Rd man/probeMis.Rd man/summary.methped.Rd
vignettes
vignettes/MethPed-vignette.Rmd

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