recipe bioconductor-methylcc

Estimate the cell composition of whole blood in DNA methylation samples

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/methylCC.html

License:

GPL-3

Recipe:

/bioconductor-methylcc/meta.yaml

A tool to estimate the cell composition of DNA methylation whole blood sample measured on any platform technology (microarray and sequencing).

package bioconductor-methylcc

versions:

1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-1

depends bioconductor-biobase:

>=2.66.0,<2.67.0

depends bioconductor-bsseq:

>=1.42.0,<1.43.0

depends bioconductor-bumphunter:

>=1.48.0,<1.49.0

depends bioconductor-flowsorted.blood.450k:

>=1.44.0,<1.45.0

depends bioconductor-genefilter:

>=1.88.0,<1.89.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19:

>=0.6.0,<0.7.0

depends bioconductor-illuminahumanmethylation450kmanifest:

>=0.4.0,<0.5.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-minfi:

>=1.52.0,<1.53.0

depends bioconductor-plyranges:

>=1.26.0,<1.27.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends r-base:

>=4.4,<4.5.0a0

depends r-dplyr:

depends r-magrittr:

depends r-quadprog:

requirements:

additional platforms:

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-methylcc

and update with::

   mamba update bioconductor-methylcc

To create a new environment, run:

mamba create --name myenvname bioconductor-methylcc

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-methylcc:<tag>

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

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