concordex

Name	concordex JSON
Version	1.0.2 JSON
	download
home_page	https://github.com/pachterlab/concordex
Summary	Identification of spatial homogeneous regions with concordex
upload_time	2024-09-30 17:48:03
maintainer	Kayla Jackson
docs_url	None
author	Kayla Jackson, A. Sina Booeshaghi, Angel Galvez-Merchan, Alexandra Kim
requires_python	>=3.9
license	MIT License Copyright (c) 2024 Pachter Lab Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
keywords	singlecell clustering spatial transcriptomics
VCS
bugtrack_url
requirements	No requirements were recorded.
Travis-CI	No Travis.
coveralls test coverage	No coveralls.

            # concordex 1.0.2

The goal of `concordex` is to identify spatial homogeneous regions (SHRs) as defined in the recent manuscript, [“Identification of spatial homogenous regions in tissues with concordex”](https://doi.org/10.1101/2023.06.28.546949). Briefly, SHRs are are domains that are homogeneous with respect to cell type composition. `concordex` relies on the the k-nearest-neighbor (kNN) graph to representing similarities between cells and uses common clustering algorithms to identify SHRs.

## Installation

`concordex` can be installed via pip
```bash
pip install git+https://github.com/pachterlab/concordex.git
```

## Usage

After installing, `concordex` can be run as follows: 
```
import scanpy as sc 
from concordex.tools import calculate_concordex

ad = sc.datasets.pbmc68k_reduced()

# Compute concordex with discrete labels
calculate_concordex(ad, 'louvain', n_neighbors=10)

# Neighborhood consolidation information is stored in `adata.obsm`
ad.obsm['nbc'][:3]

# The column names are stored in `adata.uns`
ad.uns['nbc_params']['nbc_colnames']
```

## Citation

If you’d like to use the `concordex` package in your research, please
cite our recent bioRxiv preprint

> Jackson, K.; Booeshaghi, A. S.; Gálvez-Merchán, Á.; Moses, L.; Chari,
> T.; Kim, A.; Pachter, L. Identification of spatial homogeneous regions in tissues 
> with concordex. bioRxiv (Cold Spring Harbor Laboratory) 2023. 
> <https://doi.org/10.1101/2023.06.28.546949>.

    @article {Jackson2023.06.28.546949, 
        author = {Jackson, Kayla C. and Booeshaghi, A. Sina and G{'a}lvez-Merch{'a}n, {'A}ngel and Moses, Lambda and Chari, Tara and Kim, Alexandra and Pachter, Lior}, 
        title = {Identification of spatial homogeneous regions in tissues with concordex}, 
        year = {2024}, 
        doi = {10.1101/2023.06.28.546949}, 
        publisher = {Cold Spring Harbor Laboratory}, 
        URL = {<https://www.biorxiv.org/content/early/2024/07/18/2023.06.28.546949>},
        journal = {bioRxiv} 
    }

## Maintainer

[Kayla Jackson](https://github.com/kayla-jackson)

            

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