recipe celltypist

A tool for semi-automatic cell type annotation

Homepage:

https://github.com/Teichlab/celltypist

License:

MIT / MIT

Recipe:

/celltypist/meta.yaml

Links:

doi: 10.1126/science.abl5197

package celltypist

versions:

1.6.3-0,  1.6.2-0,  1.6.1-0,  1.6.0-0,  1.5.3-1,  1.5.3-0,  1.5.2-0,  1.5.0-0,  1.3.0-0, 

1.6.3-0,  1.6.2-0,  1.6.1-0,  1.6.0-0,  1.5.3-1,  1.5.3-0,  1.5.2-0,  1.5.0-0,  1.3.0-0,  1.2.0-0,  1.1.0-0,  1.0.0-0,  0.2.1-0,  0.2.0-0,  0.1.9-0,  0.1.8-0,  0.1.7-0,  0.1.6-0,  0.1.5-0,  0.1.4-0,  0.1.3-1,  0.1.3-0

depends click:

>=7.1.2

depends leidenalg:

>=0.8.3

depends numpy:

>=1.19.0

depends openpyxl:

>=3.0.4

depends pandas:

>=1.0.5

depends python:

>=3.6

depends python-annoy:

depends requests:

>=2.23.0

depends scanpy:

>=1.7.0

depends scikit-learn:

>=0.24.1

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 celltypist

and update with::

   mamba update celltypist

To create a new environment, run:

mamba create --name myenvname celltypist

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/celltypist:<tag>

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

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