recipe bioconductor-nanostringqcpro

Quality metrics and data processing methods for NanoString mRNA gene expression data






NanoStringQCPro provides a set of quality metrics that can be used to assess the quality of NanoString mRNA gene expression data -- i.e. to identify outlier probes and outlier samples. It also provides different background subtraction and normalization approaches for this data. It outputs suggestions for flagging samples/probes and an easily sharable html quality control output.

package bioconductor-nanostringqcpro

(downloads) docker_bioconductor-nanostringqcpro



depends bioconductor-annotationdbi:


depends bioconductor-biobase:




depends r-base:


depends r-knitr:


depends r-nmf:


depends r-png:


depends r-rcolorbrewer:




You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

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-nanostringqcpro

and update with::

   mamba update bioconductor-nanostringqcpro

To create a new environment, run:

mamba create --name myenvname bioconductor-nanostringqcpro

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-nanostringqcpro/tags`_ for valid values for ``<tag>``)

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