recipe scglue

Graph-linked unified embedding for unpaired single-cell multi-omics data integration

Homepage:

https://github.com/gao-lab/GLUE

Documentation:

https://scglue.readthedocs.io

License:

MIT / MIT

Recipe:

/scglue/meta.yaml

GLUE is a flexible framework that utilizes prior knowledge about feature relations to bridge the gap between different feature spaces during unpaired multi-modal data integration.

package scglue

(downloads) docker_scglue

versions:

0.3.2-0,  0.3.1-0,  0.2.3-0,  0.2.2-0,  0.2.1-0

depends anndata:

>=0.7

depends dill:

>=0.2.3

depends h5py:

>=2.10

depends leidenalg:

>=0.7

depends matplotlib-base:

>=3.1.2

depends networkx:

>=2

depends numpy:

>=1.19,<1.22

depends packaging:

>=16.8

depends pandas:

>=1.1

depends parse:

>=1.3.2

depends pybedtools:

>=0.8.1

depends pynvml:

>=8.0.1

depends python:

>=3.6

depends pytorch:

>=1.8

depends pytorch-ignite:

>=0.4.1

depends scanpy:

>=1.5

depends scikit-learn:

>=0.21.2

depends scipy:

>=1.3

depends seaborn:

>=0.9

depends sparse:

>=0.3.1

depends statsmodels:

>=0.10

depends tensorboardx:

>=1.4

depends tqdm:

>=4.27

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 scglue

and update with::

   mamba update scglue

To create a new environment, run:

mamba create --name myenvname scglue

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/scglue:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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