- recipe bioconductor-mbased
Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection
The package implements MBASED algorithm for detecting allele-specific gene expression from RNA count data, where allele counts at individual loci (SNVs) are integrated into a gene-specific measure of ASE, and utilizes simulations to appropriately assess the statistical significance of observed ASE.
- package bioconductor-mbased¶
- depends bioconductor-biocgenerics:
- depends bioconductor-biocparallel:
- depends bioconductor-genomicranges:
- depends bioconductor-summarizedexperiment:
- depends r-base:
- depends r-runit:
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-mbased and update with:: mamba update bioconductor-mbased
To create a new environment, run:
mamba create --name myenvname bioconductor-mbased
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-mbased:<tag> (see `bioconductor-mbased/tags`_ for valid values for ``<tag>``)