recipe cytotrace2-python

CytoTRACE 2 is an interpretable AI method for predicting cellular potency and absolute developmental potential from scRNA-seq data.

Homepage:

https://github.com/digitalcytometry/cytotrace2

Documentation:

https://github.com/digitalcytometry/cytotrace2/blob/v0.0.1/cytotrace2_python/README.md

License:

Custom

Recipe:

/cytotrace2-python/meta.yaml

package cytotrace2-python

versions:

0.0.1-0

depends anndata:

depends numpy:

depends pandas:

depends python:

>=3.9

depends pytorch:

depends r-argparse:

depends r-data.table:

depends r-dplyr:

depends r-ggplot2:

depends r-matrix:

depends r-rann:

depends r-seurat:

depends r-seuratobject:

depends scanpy:

depends scikit-learn:

depends scipy:

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 cytotrace2-python

and update with::

   mamba update cytotrace2-python

To create a new environment, run:

mamba create --name myenvname cytotrace2-python

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/cytotrace2-python:<tag>

(see `cytotrace2-python/tags`_ for valid values for ``<tag>``)

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