- recipe bioconductor-xcore
xcore expression regulators inference
xcore is an R package for transcription factor activity modeling based on known molecular signatures and user's gene expression data. Accompanying xcoredata package provides a collection of molecular signatures, constructed from publicly available ChiP-seq experiments. xcore use ridge regression to model changes in expression as a linear combination of molecular signatures and find their unknown activities. Obtained, estimates can be further tested for significance to select molecular signatures with the highest predicted effect on the observed expression changes.
- package bioconductor-xcore¶
- depends bioconductor-delayedarray:
- depends bioconductor-edger:
- depends bioconductor-genomicranges:
- depends bioconductor-iranges:
- depends bioconductor-multiassayexperiment:
- depends bioconductor-s4vectors:
- depends r-base:
- depends r-foreach:
- depends r-glmnet:
- depends r-iterators:
- depends r-magrittr:
- depends r-matrix:
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-xcore and update with:: mamba update bioconductor-xcore
To create a new environment, run:
mamba create --name myenvname bioconductor-xcore
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-xcore:<tag> (see `bioconductor-xcore/tags`_ for valid values for ``<tag>``)