- recipe bioconductor-cosmosr
COSMOS (Causal Oriented Search of Multi-Omic Space)
COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets based on prior knowledge of signaling, metabolic, and gene regulatory networks. It estimated the activities of transcrption factors and kinases and finds a network-level causal reasoning. Thereby, COSMOS provides mechanistic hypotheses for experimental observations across mulit-omics datasets.
- package bioconductor-cosmosr¶
- depends bioconductor-carnival:
- depends bioconductor-dorothea:
- depends bioconductor-gseabase:
- depends r-base:
- depends r-dplyr:
- depends r-igraph:
- depends r-progress:
- depends r-purrr:
- depends r-rlang:
- depends r-stringr:
- depends r-visnetwork:
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-cosmosr and update with:: mamba update bioconductor-cosmosr
To create a new environment, run:
mamba create --name myenvname bioconductor-cosmosr
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-cosmosr:<tag> (see `bioconductor-cosmosr/tags`_ for valid values for ``<tag>``)