recipe scarches

Transfer learning with Architecture Surgery on Single-cell data

Homepage:

https://github.com/theislab/scarches

License:

BSD-3-Clause

Recipe:

/scarches/meta.yaml

Links:

doi: 10.1038/s41587-021-01001-7

package scarches

versions:

0.6.1-0

depends anndata:

>=0.7.4

depends gdown:

depends h5py:

>=2.10.0

depends leidenalg:

depends matplotlib-base:

>=3.3.1

depends muon:

depends numpy:

>=1.19.2

depends pandas:

>=1.1.2

depends python:

depends pytorch:

>=1.8.0

depends requests:

depends scanpy:

>=1.6.0

depends schpl:

>=1.0.0

depends scikit-learn:

>=0.23.2

depends scipy:

>=1.5.2

depends scvi-tools:

>=0.12.1

depends tqdm:

>=4.56.0

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 scarches

and update with::

   mamba update scarches

To create a new environment, run:

mamba create --name myenvname scarches

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/scarches:<tag>

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

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