- recipe bioconductor-buscorrect
Batch Effects Correction with Unknown Subtypes
GPL (>= 2)
High-throughput experimental data are accumulating exponentially in public databases. However, mining valid scientific discoveries from these abundant resources is hampered by technical artifacts and inherent biological heterogeneity. The former are usually termed "batch effects," and the latter is often modelled by "subtypes." The R package BUScorrect fits a Bayesian hierarchical model, the Batch-effects-correction-with-Unknown-Subtypes model (BUS), to correct batch effects in the presence of unknown subtypes. BUS is capable of (a) correcting batch effects explicitly, (b) grouping samples that share similar characteristics into subtypes, (c) identifying features that distinguish subtypes, and (d) enjoying a linear-order computation complexity.
- package bioconductor-buscorrect¶
- depends bioconductor-summarizedexperiment:
- depends libblas:
- depends libgcc-ng:
- depends liblapack:
- depends r-base:
- depends r-gplots:
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-buscorrect and update with:: mamba update bioconductor-buscorrect
To create a new environment, run:
mamba create --name myenvname bioconductor-buscorrect
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-buscorrect:<tag> (see `bioconductor-buscorrect/tags`_ for valid values for ``<tag>``)