Package Recipe 'sdeper'

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:

2.0.0-0, 1.7.1-0, 1.7.0-0, 1.6.4-1, 1.6.4-0, 1.6.3-0, 1.6.2-0, 1.6.1-0, 1.5.0-0,

2.0.0-0, 1.7.1-0, 1.7.0-0, 1.6.4-1, 1.6.4-0, 1.6.3-0, 1.6.2-0, 1.6.1-0, 1.5.0-0, 1.4.0-0, 1.3.1-0, 1.3.0-0, 1.2.1-0, 1.2.0-0, 1.1.0-0, 1.0.0-0

Depends:

on distinctipy 1.2.2
on libopencv 4.9.0 headless_*
on matplotlib-base 3.5.2
on numba 0.59.1
on numpy 1.26.4
on opencv 4.9.0
on openpyxl 3.0.10
on pandas 1.4.3
on py-opencv 4.9.0
on python >=3.9,<=3.10
on reportlab 4.1.0
on scanpy 1.9.1
on scikit-learn 1.1.1
on scikit-misc 0.1.4
on scipy 1.11.4
on seaborn 0.13.2
on tensorflow-base 2.15.0 cpu_*
on umap-learn 0.5.3

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install sdeper

to add into an existing workspace instead, run:

pixi add sdeper

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install sdeper

Alternatively, to install into a new environment, run:

conda create -n envname sdeper

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

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/sdeper/README.html)