- recipe bioconductor-affyrnadegradation
Analyze and correct probe positional bias in microarray data due to RNA degradation
The package helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.
- package bioconductor-affyrnadegradation¶
- depends bioconductor-affy:
- depends r-base:
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-affyrnadegradation and update with:: mamba update bioconductor-affyrnadegradation
To create a new environment, run:
mamba create --name myenvname bioconductor-affyrnadegradation
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-affyrnadegradation:<tag> (see `bioconductor-affyrnadegradation/tags`_ for valid values for ``<tag>``)