recipe decifer

DeCiFer simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell fractions (DCF)

Homepage:

https://github.com/raphael-group/decifer

License:

BSD-3

Recipe:

/decifer/meta.yaml

DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell fractions (DCF), a statistic that quantifies the proportion of cells which acquired the SNV or whose ancestors acquired the SNV. DCF is related to the commonly used cancer cell fraction (CCF) but further accounts for SNVs which are lost due to deleterious somatic copy-number aberrations (CNAs), identifying clusters of SNVs which occur in the same phylogenetic branch of tumour evolution.

package decifer

versions:

2.1.4-0,  2.1.3-0,  2.1.2-1,  2.1.2-0,  2.1.1-0,  2.1.0-0,  2.0.5-1,  2.0.5-0,  2.0.4-0, 

2.1.4-0,  2.1.3-0,  2.1.2-1,  2.1.2-0,  2.1.1-0,  2.1.0-0,  2.0.5-1,  2.0.5-0,  2.0.4-0,  2.0.3-0,  2.0.2-0,  2.0.1-0,  1.1.5-0,  1.1.4-0,  1.1-0,  1.0.0-0,  0.0.2-1,  0.0.2-0

depends lemon:

>=1.3.1,<1.3.2.0a0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends numpy:

>=1.16.1

depends pandas:

depends python:

>=3.11,<3.12.0a0

depends python_abi:

3.11.* *_cp311

depends scipy:

>=1.2.1

depends seaborn:

>=0.7.1

requirements:

Installation

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 decifer

and update with::

   mamba update decifer

To create a new environment, run:

mamba create --name myenvname decifer

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 quay.io/biocontainers/decifer:<tag>

(see `decifer/tags`_ for valid values for ``<tag>``)

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