recipe sdeper

Spatial Deconvolution method with Platform Effect Removal

Homepage:

https://az7jh2.github.io/SDePER/

Documentation:

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

Developer docs:

https://github.com/az7jh2/SDePER

License:

MIT / MIT

Recipe:

/sdeper/meta.yaml

SDePER (Spatial Deconvolution method with Platform Effect Removal) is a hybrid machine learning and regression method to deconvolve Spatial barcoding-based transcriptomic data using reference single-cell RNA sequencing data, considering platform effects removal, sparsity of cell types per capture spot and across-spots spatial correlation in cell type compositions. SDePER is also able to impute cell type compositions and gene expression at unmeasured locations in a tissue map with enhanced resolution.

package sdeper

versions:

1.2.1-0,  1.2.0-0,  1.1.0-0,  1.0.0-0

depends distinctipy:

1.2.2

depends libopencv:

4.6.0

depends matplotlib-base:

3.5.2

depends networkx:

2.8.4

depends numba:

0.55.2

depends numpy:

1.22.4

depends opencv:

4.6.0

depends openpyxl:

3.0.10

depends pandas:

1.4.3

depends py-opencv:

4.6.0

depends python:

>=3.9.12,<3.11

depends reportlab:

4.1.0

depends scanpy:

1.9.1

depends scikit-learn:

1.1.1

depends scikit-misc:

0.1.4

depends scipy:

1.8.1

depends seaborn:

0.11.2

depends tensorflow-base:

2.9.1 cpu_*

depends umap-learn:

0.5.3

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 sdeper

and update with::

   mamba update sdeper

To create a new environment, run:

mamba create --name myenvname sdeper

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/sdeper:<tag>

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

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