recipe tpmcalculator

TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files.



Public Domain



package tpmcalculator

(downloads) docker_tpmcalculator



depends bamtools:


depends libgcc-ng:


depends libstdcxx-ng:


depends libzlib:


depends zlib:



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 tpmcalculator

and update with::

   mamba update tpmcalculator

To create a new environment, run:

mamba create --name myenvname tpmcalculator

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

Download stats