MethPed specifications

Information


Unique identifier OMICS_12934
Name MethPed
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.8.0
Stability Stable
Requirements
stats, graphics, Biobase, BiocStyle, grDevices, knitr, R(>=3.0.0), randomforest, impute, markdown
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Helena Carén

Publications for MethPed

MethPed citations

 (2)
library_books

Establishment and characterization of an orthotopic patient derived Group 3 medulloblastoma model for preclinical drug evaluation

2017
Sci Rep
PMCID: 5394470
PMID: 28417956
DOI: 10.1038/srep46366

[…] signals were preprocessed and normalized with the preprocessIllumina command and data quality was evaluated using the getQC feature. Normalized beta values were used to classify the samples using the MethPed algorithm, to generate PCA plots, and to perform unsupervised hierarchical clustering. Copy number profiles are based on the Bioconductor package conumee and were generated using a publicly av […]

library_books

Stem cell cultures derived from pediatric brain tumors accurately model the originating tumors

2017
Oncotarget
PMCID: 5386635
PMID: 28148893
DOI: 10.18632/oncotarget.14826

[…] d closely together with the primary tumor they were derived from, also at later passages, showing that the cells are not considerably altered in our culture system.We next used our recently developed MethPed brain tumor classifier [] to investigate if the cultured cells retain the original brain tumor classification (Figure ). All tumors showed a strong correlation with the GBM group of tumors whi […]

MethPed institution(s)
Sahlgrenska Cancer Center, Department of Pathology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Sahlgrenska Cancer Center, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Swedish Hip Arthroplasty Register, Centre of Registers Västra Götaland, Gothenburg, Gothenburg, Sweden
MethPed funding source(s)
This work was supported by the Swedish Cancer Society; the Swedish Children’s Cancer Society; the Swedish Research Council; the Swedish Society for Medical Research; a Marie Curie CIG from the EU’s Seventh Framework Programme (FP7) and the Wenner-Gren foundation.

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