- recipe bioconductor-blima
Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level
Package blima includes several algorithms for the preprocessing of Illumina microarray data. It focuses to the bead level analysis and provides novel approach to the quantile normalization of the vectors of unequal lengths. It provides variety of the methods for background correction including background subtraction, RMA like convolution and background outlier removal. It also implements variance stabilizing transformation on the bead level. There are also implemented methods for data summarization. It also provides the methods for performing T-tests on the detector (bead) level and on the probe level for differential expression testing.
- package bioconductor-blima¶
- depends bioconductor-beadarray:
- depends bioconductor-biobase:
- depends bioconductor-biocgenerics:
- depends libblas:
- depends libgcc-ng:
- depends liblapack:
- depends libstdcxx-ng:
- depends r-base:
- 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-blima and update with:: mamba update bioconductor-blima
To create a new environment, run:
mamba create --name myenvname bioconductor-blima
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-blima:<tag> (see `bioconductor-blima/tags`_ for valid values for ``<tag>``)