easydecon 0.1.0a0__tar.gz

easydecon-0.1.0a0/LICENSE

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+MIT License
+
+Copyright (c) 2024 Sinan U. Umu
+
+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.

easydecon-0.1.0a0/PKG-INFO

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+Metadata-Version: 2.1
+Name: easydecon
+Version: 0.1.0a0
+Summary: easydecon
+Home-page: https://github.com/sinanugur/easydecon
+Author: Sinan U. Umu
+Author-email: sinanugur@gmail.com
+Keywords: scRNA single-cell high definition spatial transcriptomics deconvolution
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: scipy
+Requires-Dist: regex
+Requires-Dist: matplotlib
+Requires-Dist: pandas==2.2.2
+Requires-Dist: numpy
+Requires-Dist: stardist
+Requires-Dist: spatialdata==0.2.2
+Requires-Dist: spatialdata-io==0.1.4
+Requires-Dist: spatialdata-plot==0.2.4
+Requires-Dist: xarray-spatial==0.4.0
+Requires-Dist: ipykernel
+Requires-Dist: squidpy
+Requires-Dist: joblib
+Requires-Dist: napari
+Requires-Dist: napari-spatialdata
+Requires-Dist: napari[pyqt6_experimental]
+Requires-Dist: xlrd==2.0.1
+
+# Easydecon
+
+A package to analyze celltypes on high definition spatial profiling assays
+
+Installation
+------------
+It is recommended to install the package in a virtual environment or a Conda environment. To create a Conda environment, run the following command:
+
+```bash
+conda create -n easydecon python=3.11
+conda activate easydecon
+```
+
+To install directly from GitHub using pip into the active environment, run the following command:
+
+```bash
+pip install git+https://github.com/sinanugur/easydecon.git
+```
+
+
+Usage and Documentation
+-----------------------
+You may find our example notebooks in the `notebooks` folder.
+
+- Demo notebook for a single-cell Anndata object (demo)[https://github.com/sinanugur/easydecon/blob/main/notebooks/demo.ipynb]
+- Demo notebook for macrophage markers (demo_macrophage)[https://github.com/sinanugur/easydecon/blob/main/notebooks/demo_macrophage.ipynb]

easydecon-0.1.0a0/README.md

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+# Easydecon
+
+A package to analyze celltypes on high definition spatial profiling assays
+
+Installation
+------------
+It is recommended to install the package in a virtual environment or a Conda environment. To create a Conda environment, run the following command:
+
+```bash
+conda create -n easydecon python=3.11
+conda activate easydecon
+```
+
+To install directly from GitHub using pip into the active environment, run the following command:
+
+```bash
+pip install git+https://github.com/sinanugur/easydecon.git
+```
+
+
+Usage and Documentation
+-----------------------
+You may find our example notebooks in the `notebooks` folder.
+
+- Demo notebook for a single-cell Anndata object (demo)[https://github.com/sinanugur/easydecon/blob/main/notebooks/demo.ipynb]
+- Demo notebook for macrophage markers (demo_macrophage)[https://github.com/sinanugur/easydecon/blob/main/notebooks/demo_macrophage.ipynb]

easydecon-0.1.0a0/easydecon/config.py

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+class Config:
+    n_jobs = 5  # Default value
+    batch_size = 1000  # Default value    
+
+config = Config()
+
+def set_n_jobs(n):
+    config.n_jobs = n
+
+def set_batch_size(n):
+    config.batch_size = n