- recipe bioconductor-consensusov
Gene expression-based subtype classification for high-grade serous ovarian cancer
This package implements four major subtype classifiers for high-grade serous (HGS) ovarian cancer as described by Helland et al. (PLoS One, 2011), Bentink et al. (PLoS One, 2012), Verhaak et al. (J Clin Invest, 2013), and Konecny et al. (J Natl Cancer Inst, 2014). In addition, the package implements a consensus classifier, which consolidates and improves on the robustness of the proposed subtype classifiers, thereby providing reliable stratification of patients with HGS ovarian tumors of clearly defined subtype.
- package bioconductor-consensusov¶
- depends bioconductor-biobase:
- depends bioconductor-genefu:
- depends bioconductor-gsva:
- depends bioconductor-limma:
- depends r-base:
- depends r-gdata:
- depends r-matrixstats:
- depends r-randomforest:
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-consensusov and update with:: mamba update bioconductor-consensusov
To create a new environment, run:
mamba create --name myenvname bioconductor-consensusov
myenvnamebeing 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-consensusov:<tag> (see `bioconductor-consensusov/tags`_ for valid values for ``<tag>``)