- recipe bioconductor-harman
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
GPL-3 + file LICENCE
Harman is a PCA and constrained optimisation based technique that maximises the removal of batch effects from datasets, with the constraint that the probability of overcorrection (i.e. removing genuine biological signal along with batch noise) is kept to a fraction which is set by the end-user.
- package bioconductor-harman¶
- depends libblas:
- depends libgcc-ng:
- depends liblapack:
- depends libstdcxx-ng:
- depends r-base:
- depends r-ckmeans.1d.dp:
- depends r-matrixstats:
- depends r-rcpp:
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-harman and update with:: mamba update bioconductor-harman
To create a new environment, run:
mamba create --name myenvname bioconductor-harman
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-harman:<tag> (see `bioconductor-harman/tags`_ for valid values for ``<tag>``)