recipe bioconductor-methped

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

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/MethPed.html

License:

GPL-2

Recipe:

/bioconductor-methped/meta.yaml

Links:

biotools: methped, doi: 10.1186/s13148-015-0103-3

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).

package bioconductor-methped

(downloads) docker_bioconductor-methped

versions:
1.30.0-0,  1.28.0-0,  1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0, 

1.30.0-0,  1.28.0-0,  1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.10.1-0,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends r-base:

>=4.3,<4.4.0a0

depends r-randomforest:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-methped

and update with::

   mamba update bioconductor-methped

To create a new environment, run:

mamba create --name myenvname bioconductor-methped

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-methped:<tag>

(see `bioconductor-methped/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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