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توضیحات

A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.

ویژگی	مقدار
سیستم عامل	-
نام فایل	cellcharter-0.1.2
نام	cellcharter
نسخه کتابخانه	0.1.2
نگهدارنده	[]
ایمیل نگهدارنده	['Marco Varrone <marco.varrone@unil.ch>']
نویسنده	CSO group
ایمیل نویسنده	-
آدرس صفحه اصلی	-
آدرس اینترنتی	https://pypi.org/project/cellcharter/
مجوز	BSD 3-Clause License Copyright (c) 2022, Marco Varrone All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

<div align="center"> <img src="https://github.com/CSOgroup/cellcharter/raw/main/docs/_static/cellcharter.png" width="400px"> **A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.** --- <a href="https://cellcharter.readthedocs.io/en/latest/" target="_blank">Documentation</a> • <a href="https://cellcharter.readthedocs.io/en/latest/notebooks/codex_mouse_spleen.html" target="_blank">Examples</a> • <a href="https://www.biorxiv.org/content/10.1101/2023.01.10.523386v1" target="_blank">Paper</a> [![Tests][badge-tests]][link-tests] [![Documentation][badge-docs]][link-docs] [badge-tests]: https://img.shields.io/github/actions/workflow/status/CSOgroup/cellcharter/test.yaml?branch=main [link-tests]: https://github.com/CSOgroup/cellcharter/actions/workflows/test.yml [badge-docs]: https://img.shields.io/readthedocs/cellcharter </div> ## Background Spatial clustering determines cellular niches characterized by specific admixing of these populations. It assigns cells to clusters based on both their intrinsic features (e.g., protein or mRNA expression), and the features of neighboring cells in the tissue. <img src="https://github.com/CSOgroup/cellcharter/raw/main/docs/_static/spatial_clusters.png" width="500px"> CellCharter is able to automatically identify spatial clusters, and offers a suite of approaches for cluster characterization and comparison. <img src="https://github.com/CSOgroup/cellcharter/raw/main/docs/_static/cellcharter_workflow.png" width="800px"> ## Getting started Please refer to the [documentation][link-docs]. In particular, the - [API documentation][link-api]. - [Tutorials][link-tutorial] ## Installation CellCharter uses Python < 3.11 and [PyTorch](https://pytorch.org) <= 1.12.1. If you are planning to use a GPU, make sure to download and install the correct version of PyTorch first. In CellCharter, only the dimensionality reduction and batch correction step is dependent on the data type. In particular, it uses: - [scVI](https://github.com/scverse/scvi-tools) for spatial transcriptomics data such as 10x Visium and Xenium, Nanostring CosMx, Vizgen MERSCOPE, Stereo-seq, DBiT-seq, MERFISH and seqFISH data. - A modified version of [scArches](https://github.com/theislab/scarches)'s TRVAE model for spatial proteomics data such as Akoya CODEX, Lunaphore COMET, CyCIF, IMC and MIBI-TOF data. By installing CellCharter without specifying the type of data, as in the following code, it will install without any of the two models. ```bash pip install cellcharter ``` However, you can include in the installation the type of data (transcriptomics and/or proteomics) you are planning to analyze, and it will install the required dependencies. ```bash pip install cellcharter[transcriptomics] ``` ## Contribution If you found a bug or you want to propose a new feature, please use the [issue tracker][issue-tracker]. [issue-tracker]: https://github.com/CSOgroup/cellcharter/issues [link-docs]: https://cellcharter.readthedocs.io [link-api]: https://cellcharter.readthedocs.io/en/latest/api.html [link-tutorial]: https://cellcharter.readthedocs.io/en/latest/notebooks/codex_mouse_spleen.html

نیازمندی

مقدار	نام
-	anndata
-	pycave
-	scikit-learn
-	session-info
-	squidpy
xtr	bump2version;
xtr	pre-commit;
xtr	twine>=4.0.2;
xtr	ipykernel;
xtr	ipython;
xtr	myst-nb;
xtr	sphinx-autodoc-typehints;
xtr	sphinx-book-theme>=0.3.3;
xtr	sphinx-copybutton;
xtr	sphinx>=4;
xtr	sphinxcontrib-bibtex>=1.0.0;
xtr	scarches;
xtr	pytest;
xtr	pytest-cov;
xtr	pytest-order;
xtr	scvi-tools;

زبان مورد نیاز

مقدار	نام
<3.11,>=3.8	Python

نحوه نصب

نصب پکیج whl cellcharter-0.1.2:

pip install cellcharter-0.1.2.whl

نصب پکیج tar.gz cellcharter-0.1.2:

pip install cellcharter-0.1.2.tar.gz