- recipe bioconductor-degraph
Two-sample tests on a graph
DEGraph implements recent hypothesis testing methods which directly assess whether a particular gene network is differentially expressed between two conditions. This is to be contrasted with the more classical two-step approaches which first test individual genes, then test gene sets for enrichment in differentially expressed genes. These recent methods take into account the topology of the network to yield more powerful detection procedures. DEGraph provides methods to easily test all KEGG pathways for differential expression on any gene expression data set and tools to visualize the results.
- package bioconductor-degraph¶
- depends bioconductor-graph:
- depends bioconductor-kegggraph:
- depends bioconductor-ncigraph:
- depends bioconductor-rbgl:
- depends bioconductor-rgraphviz:
- depends r-base:
- depends r-lattice:
- depends r-mvtnorm:
- depends r-r.methodss3:
- depends r-r.utils:
- depends r-rrcov:
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-degraph and update with:: mamba update bioconductor-degraph
To create a new environment, run:
mamba create --name myenvname bioconductor-degraph
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-degraph:<tag> (see `bioconductor-degraph/tags`_ for valid values for ``<tag>``)