SURE-tools 2.2.4__tar.gz

sure_tools-2.2.4/LICENSE

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+MIT License
+
+Copyright (c) 2024 ZengFLab
+
+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,
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+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

sure_tools-2.2.4/PKG-INFO

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+Metadata-Version: 2.4
+Name: SURE-tools
+Version: 2.2.4
+Summary: Succinct Representation of Single Cells
+Home-page: https://github.com/ZengFLab/SURE
+Author: Feng Zeng
+Author-email: zengfeng@xmu.edu.cn
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: dill==0.3.8
+Requires-Dist: scanpy
+Requires-Dist: pytorch-ignite
+Requires-Dist: datatable
+Requires-Dist: scipy
+Requires-Dist: numpy
+Requires-Dist: scikit-learn
+Requires-Dist: pandas
+Requires-Dist: pyro-ppl
+Requires-Dist: jax[cuda12]
+Requires-Dist: leidenalg
+Requires-Dist: python-igraph
+Requires-Dist: networkx
+Requires-Dist: matplotlib
+Requires-Dist: seaborn
+Requires-Dist: fa2-modified
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+# SURE: SUccinct REpresentation of cells
+ SURE introduces a vector quantization-based probabilistic generative model for calling metacells and use them as landmarks that form a coordinate system for cell ID. Analyzing single-cell omics data in a manner analogous to reference genome-based genomic analysis.
+
+## **$$\color{red}\text{\textbf{UPDATE}}$$**
+An update has been distributed. Users can access to it via [SUREv2](https://github.com/ZengFLab/SUREv2). It provides Python classes that users can call SURE in scripts. It also provide the command that users can run SURE in the shell. Additionally, SUREv2 supports the calling of metacells for multi-omics datasets.
+
+## Installation
+1. Create a virtual environment
+```bash
+conda create -n SUREv1 python=3.10 scipy numpy pandas scikit-learn && conda activate SUREv1
+```
+
+2. Install [PyTorch](https://pytorch.org/get-started/locally/) following the official instruction. 
+```bash
+pip3 install torch torchvision --index-url https://download.pytorch.org/whl/cu126
+```
+
+3. Install SURE
+```bash
+pip3 install SURE-tools
+```
+
+## Example 1: Calling metacells for a single-cell dataset
+
+Users can refer to [here](https://github.com/ZengFLab/SURE_example_1) for details.
+
+## Example 2: The hierarchical assembly of large-scale dataset(s)
+
+Users can refer to [here](https://github.com/ZengFLab/SURE_example_2) for details.
+
+## Example 3: Human brain cell atlas
+
+Users can refer to [here](https://github.com/ZengFLab/SURE_example_3) for details.
+
+## Example 4: Metacell calling for scATAC-seq data
+
+Users can refer to [here](https://github.com/ZengFLab/SURE_example_4) for details.
+
+

sure_tools-2.2.4/README.md

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+# SURE: SUccinct REpresentation of cells
+ SURE introduces a vector quantization-based probabilistic generative model for calling metacells and use them as landmarks that form a coordinate system for cell ID. Analyzing single-cell omics data in a manner analogous to reference genome-based genomic analysis.
+
+## **$$\color{red}\text{\textbf{UPDATE}}$$**
+An update has been distributed. Users can access to it via [SUREv2](https://github.com/ZengFLab/SUREv2). It provides Python classes that users can call SURE in scripts. It also provide the command that users can run SURE in the shell. Additionally, SUREv2 supports the calling of metacells for multi-omics datasets.
+
+## Installation
+1. Create a virtual environment
+```bash
+conda create -n SUREv1 python=3.10 scipy numpy pandas scikit-learn && conda activate SUREv1
+```
+
+2. Install [PyTorch](https://pytorch.org/get-started/locally/) following the official instruction. 
+```bash
+pip3 install torch torchvision --index-url https://download.pytorch.org/whl/cu126
+```
+
+3. Install SURE
+```bash
+pip3 install SURE-tools
+```
+
+## Example 1: Calling metacells for a single-cell dataset
+
+Users can refer to [here](https://github.com/ZengFLab/SURE_example_1) for details.
+
+## Example 2: The hierarchical assembly of large-scale dataset(s)
+
+Users can refer to [here](https://github.com/ZengFLab/SURE_example_2) for details.
+
+## Example 3: Human brain cell atlas
+
+Users can refer to [here](https://github.com/ZengFLab/SURE_example_3) for details.
+
+## Example 4: Metacell calling for scATAC-seq data
+
+Users can refer to [here](https://github.com/ZengFLab/SURE_example_4) for details.
+
+