recipe bioconductor-flowsorted.blood.epic

Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells

Homepage:

https://bioconductor.org/packages/3.18/data/experiment/html/FlowSorted.Blood.EPIC.html

License:

GPL-3

Recipe:

/bioconductor-flowsorted.blood.epic/meta.yaml

Raw data objects to be used for blood cell proportion estimation in minfi and similar packages. The FlowSorted.Blood.EPIC object is based in samples assayed by Brock Christensen and colleagues; for details see Salas et al. 2018. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110554.

package bioconductor-flowsorted.blood.epic

(downloads) docker_bioconductor-flowsorted.blood.epic

versions:
2.6.0-0,  2.4.2-0,  2.2.0-0,  1.12.1-1,  1.12.1-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.1-0, 

2.6.0-0,  2.4.2-0,  2.2.0-0,  1.12.1-1,  1.12.1-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.1-0,  1.4.0-0,  1.2.0-1,  1.0.0-0

depends bioconductor-annotationhub:

>=3.10.0,<3.11.0

depends bioconductor-data-packages:

>=20231203

depends bioconductor-experimenthub:

>=2.10.0,<2.11.0

depends bioconductor-genefilter:

>=1.84.0,<1.85.0

depends bioconductor-minfi:

>=1.48.0,<1.49.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends curl:

depends r-base:

>=4.3,<4.4.0a0

depends r-nlme:

depends r-quadprog:

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-flowsorted.blood.epic

and update with::

   mamba update bioconductor-flowsorted.blood.epic

To create a new environment, run:

mamba create --name myenvname bioconductor-flowsorted.blood.epic

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-flowsorted.blood.epic:<tag>

(see `bioconductor-flowsorted.blood.epic/tags`_ for valid values for ``<tag>``)

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