recipe bioconductor-lungcanceracvssccgeo

A lung cancer dataset that can be used with maPredictDSC package for developing outcome prediction models from Affymetrix CEL files.

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-lungcanceracvssccgeo/meta.yaml

This package contains 30 Affymetrix CEL files for 7 Adenocarcinoma (AC) and 8 Squamous cell carcinoma (SCC) lung cancer samples taken at random from 3 GEO datasets (GSE10245, GSE18842 and GSE2109) and other 15 samples from a dataset produced by the organizers of the IMPROVER Diagnostic Signature Challenge available from GEO (GSE43580).

package bioconductor-lungcanceracvssccgeo

(downloads) docker_bioconductor-lungcanceracvssccgeo

versions:
1.38.0-0,  1.36.0-0,  1.34.0-1,  1.33.0-0,  1.30.0-1,  1.30.0-0,  1.28.0-0,  1.26.0-3,  1.26.0-2, 

1.38.0-0,  1.36.0-0,  1.34.0-1,  1.33.0-0,  1.30.0-1,  1.30.0-0,  1.28.0-0,  1.26.0-3,  1.26.0-2,  1.26.0-1,  1.26.0-0,  1.25.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-0

depends bioconductor-data-packages:

>=20231203

depends curl:

depends r-base:

>=4.3,<4.4.0a0

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-lungcanceracvssccgeo

and update with::

   mamba update bioconductor-lungcanceracvssccgeo

To create a new environment, run:

mamba create --name myenvname bioconductor-lungcanceracvssccgeo

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-lungcanceracvssccgeo:<tag>

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

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