recipe palantir

Palantir for modeling continuous cell state and cell fate choices in single cell data

Homepage:

https://github.com/dpeerlab/palantir

Documentation:

https://palantir.readthedocs.io

License:

GPL / GPL-2.0-only

Recipe:

/palantir/meta.yaml

package palantir

versions:

1.3.4-0,  1.3.3-0

depends anndata:

>=0.8.0

depends fcsparser:

>=0.1.2

depends joblib:

depends leidenalg:

>=0.9.1

depends matplotlib-base:

>=2.2.2

depends mellon:

>=1.3.0

depends networkx:

>=2.1

depends numpy:

>=1.14.2

depends pandas:

>=0.22.0

depends pygam:

depends python:

depends scanpy:

>=1.6.0

depends scikit-learn:

depends scipy:

>=1.3

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 palantir

and update with::

   mamba update palantir

To create a new environment, run:

mamba create --name myenvname palantir

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/palantir:<tag>

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

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