recipe bioconductor-harmonizr

Handles missing values and makes more data available

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-harmonizr/meta.yaml

An implementation, which takes input data and makes it available for proper batch effect removal by ComBat or Limma. The implementation appropriately handles missing values by dissecting the input matrix into smaller matrices with sufficient data to feed the ComBat or limma algorithm. The adjusted data is returned to the user as a rebuild matrix. The implementation is meant to make as much data available as possible with minimal data loss.

package bioconductor-harmonizr

versions:

1.0.0-0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-sva:

>=3.50.0,<3.51.0

depends r-base:

>=4.3,<4.4.0a0

depends r-doparallel:

>=1.0.16

depends r-foreach:

>=1.5.1

depends r-janitor:

>=2.1.0

depends r-plyr:

>=1.8.6

depends r-seriation:

>=1.3.5

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-harmonizr

and update with::

   mamba update bioconductor-harmonizr

To create a new environment, run:

mamba create --name myenvname bioconductor-harmonizr

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-harmonizr:<tag>

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

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