recipe bioconductor-fieldeffectcrc

Tumor, tumor-adjacent normal, and healthy colorectal transcriptomes as SummarizedExperiment objects

Homepage:

https://bioconductor.org/packages/3.18/data/experiment/html/FieldEffectCrc.html

License:

Artistic-2.0

Recipe:

/bioconductor-fieldeffectcrc/meta.yaml

Processed RNA-seq data for 1,139 human primary colorectal tissue samples across three phenotypes, including tumor, normal adjacent-to-tumor, and healthy, available as Synapse ID syn22237139 on synapse.org. Data have been parsed into SummarizedExperiment objects available via ExperimentHub to facilitate reproducibility and extension of results from Dampier et al. (PMCID: PMC7386360, PMID: 32764205).

package bioconductor-fieldeffectcrc

versions:

1.12.0-0,  1.10.0-0,  1.8.0-0,  1.4.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-1,  1.0.0-0

depends bioconductor-annotationhub:

>=3.10.0,<3.11.0

depends bioconductor-biocstyle:

>=2.30.0,<2.31.0

depends bioconductor-data-packages:

>=20231203

depends bioconductor-deseq2:

>=1.42.0,<1.43.0

depends bioconductor-experimenthub:

>=2.10.0,<2.11.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends curl:

depends r-base:

>=4.3,<4.4.0a0

depends r-runit:

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-fieldeffectcrc

and update with::

   mamba update bioconductor-fieldeffectcrc

To create a new environment, run:

mamba create --name myenvname bioconductor-fieldeffectcrc

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-fieldeffectcrc:<tag>

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

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