- recipe bioconductor-bifet
Bias-free Footprint Enrichment Test
BiFET identifies TFs whose footprints are over-represented in target regions compared to background regions after correcting for the bias arising from the imbalance in read counts and GC contents between the target and background regions. For a given TF k, BiFET tests the null hypothesis that the target regions have the same probability of having footprints for the TF k as the background regions while correcting for the read count and GC content bias. For this, we use the number of target regions with footprints for TF k, t_k as a test statistic and calculate the p-value as the probability of observing t_k or more target regions with footprints under the null hypothesis.
- package bioconductor-bifet¶
- depends bioconductor-genomicranges:
- depends r-base:
- depends r-poibin:
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-bifet and update with:: mamba update bioconductor-bifet
To create a new environment, run:
mamba create --name myenvname bioconductor-bifet
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-bifet:<tag> (see `bioconductor-bifet/tags`_ for valid values for ``<tag>``)