recipe merfishtools

MERFISHtools implement a Bayesian framework for accurately predicting gene or transcript expression from MERFISH data. On top, differential expression analysis can be performed for two or multiple conditions, including credible intervals for fold change and coefficient of variation, and controlling the expected false discovery rate.






package merfishtools

(downloads) docker_merfishtools



depends gsl:


depends libgcc-ng:


depends matplotlib:

depends numpy:

depends openblas:


depends pandas:

depends python:




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 merfishtools

and update with::

   mamba update merfishtools

To create a new environment, run:

mamba create --name myenvname merfishtools

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 `merfishtools/tags`_ for valid values for ``<tag>``)

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