recipe cdna_cupcake

cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data.



BSD / BSD-3-Clause-Clear



package cdna_cupcake

(downloads) docker_cdna_cupcake



depends bcbio-gff:

depends biopython:

depends bx-python:


depends graphviz:

depends libgcc-ng:


depends numpy:


depends pysam:

depends python:


depends python_abi:

3.10.* *_cp310

depends r-base:

depends samtools:


depends scikit-learn:



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 cdna_cupcake

and update with::

   mamba update cdna_cupcake

To create a new environment, run:

mamba create --name myenvname cdna_cupcake

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

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