recipe scanpy

Single-Cell Analysis in Python. Scales to >1M cells.

Homepage

https://scanpy.readthedocs.io/en/latest/

Developer docs

http://github.com/theislab/scanpy

License

BSD / BSD-3

Recipe

/scanpy/meta.yaml

Links

doi: 10.1186/s13059-017-1382-0, usegalaxy-eu: scanpy_cluster_reduce_dimension

package scanpy

Versions

1.6.0-0,  1.5.1-0,  1.5.0-0,  1.4.6-0,  1.4.4.post1-3,  1.4.4.post1-2,  1.4.4.post1-1,  1.4.4.post1-0,  1.4.4-1, 

1.6.0-0,  1.5.1-0,  1.5.0-0,  1.4.6-0,  1.4.4.post1-3,  1.4.4.post1-2,  1.4.4.post1-1,  1.4.4.post1-0,  1.4.4-1,  1.4.4-0,  1.4.3-0,  1.4.2-0,  1.4.1-0,  1.4-0,  1.3.7-0,  1.3.6-0,  1.3.5-0,  1.3.4-0,  1.3.3-0,  1.3.2-0,  1.3.1-0

Depends

• anndata >=0.7

• h5py >=2.10.0

• importlib_metadata >=0.7

• joblib

• legacy-api-wrap

• matplotlib-base >=3.1.2

• natsort

• networkx

• numba >=0.41.0

• packaging

• pandas >=0.21

• patsy

• pytables

• python >=3.6

• scikit-learn >=0.21.2

• scipy >=1.3

• seaborn

• setuptools_scm

• sinfo

• statsmodels >=0.10.0rc2

• tqdm

• umap-learn >=0.3.10

Required By

• scvelo

• cellrank

• scaden

• scelvis

• scanpy-scripts

• scvi

• scirpy

• dca

• sccaf

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install scanpy

and update with:

conda update scanpy

or use the docker container:

docker pull quay.io/biocontainers/scanpy:<tag>

(see scanpy/tags for valid values for <tag>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/scanpy/README.html)