recipe switchtfi

Implementation of the SwitchTFI method as presented in: https://doi.org/10.1101/2025.01.20.633856

Homepage:

https://github.com/bionetslab/SwitchTFI

Documentation:

https://github.com/bionetslab/SwitchTFI#readme

License:

GPL-3.0-only

Recipe:

/switchtfi/meta.yaml

package switchtfi

versions:

0.1.0-0

depends anndata:

>=0.8

depends graph-tool:

>=2.45

depends leidenalg:

>=0.10

depends magic-impute:

>=3.0.0

depends matplotlib-base:

>=3.5

depends networkx:

>=3.0

depends numpy:

>=1.26

depends pandas:

>=2.1

depends pillow:

>=9.0

depends pymupdf:

>=1.20

depends python:

>=3.9,<3.13

depends python-igraph:

>=0.10

depends scanpy:

>=1.9

depends scikit-learn:

>=1.5

depends scipy:

>=1.10

depends seaborn:

>=0.12

depends statsmodels:

>=0.13

requirements:

additional platforms:

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 switchtfi

and update with::

   mamba update switchtfi

To create a new environment, run:

mamba create --name myenvname switchtfi

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/switchtfi:<tag>

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

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