Introduction | Necessary packages and installation guide | Input data type and format for the MethPed classifier | Input data type | Input data format | ExpressionSet class | matrix class | data.frame class | Workflow of MethPed classifier | A working example of MethPed | Dataset without missing probe values | Check missing value in data | Apply the MethPed classifier | Output summary | Output visualization | Count missing probes | Dataset with missing probe values | Missing beta value in the data set | Missing values imputation | Contact and Citation | Contact | Citation | Authors information | Session info | References
Package: MethPed 1.41.0
Helena Carén
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).
Authors:
MethPed_1.41.0.tar.gz
MethPed_1.41.0.zip(r-4.7)MethPed_1.41.0.zip(r-4.6)MethPed_1.41.0.zip(r-4.5)
MethPed_1.41.0.tgz(r-4.6-any)MethPed_1.41.0.tgz(r-4.5-any)
MethPed_1.41.0.tar.gz(r-4.7-any)MethPed_1.41.0.tar.gz(r-4.6-any)
MethPed_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
MethPed/json (API)
| # Install 'MethPed' in R: |
| install.packages('MethPed', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- MethPed_900probes - List of 900 probes in the predictor data
- MethPed_sample - Sample dataset to MethPed package.
On BioConductor:MethPed-1.41.0(bioc 3.24)MethPed-1.40.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologydnamethylationclassificationepigenetics
Last updated from:acad6ae20b. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 147 | ||
| linux-devel-x86_64 | OK | 243 | ||
| source / vignettes | OK | 230 | ||
| linux-release-x86_64 | OK | 269 | ||
| macos-release-arm64 | OK | 213 | ||
| macos-oldrel-arm64 | OK | 195 | ||
| windows-devel | OK | 182 | ||
| windows-release | OK | 179 | ||
| windows-oldrel | OK | 183 | ||
| wasm-release | OK | 100 |
Exports:checkNAMethPedprobeMis
Dependencies:BiobaseBiocGenericsgenericsrandomForest
