pycrosstalker 0.1.0__tar.gz

pycrosstalker-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2024 CostaLab
+
+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.

pycrosstalker-0.1.0/PKG-INFO

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+Metadata-Version: 2.3
+Name: pycrosstalker
+Version: 0.1.0
+Summary: 
+License: MIT
+Author: jsnagai
+Author-email: james.nagai@gmail.com
+Requires-Python: >=3.10,<4.0
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: adjustText (>=1.2.0,<2.0.0)
+Requires-Dist: attrs (>=25.3.0,<26.0.0)
+Requires-Dist: gprofiler-official (==1.0.0)
+Requires-Dist: igraph (>=0.11.6,<0.12.0)
+Requires-Dist: matplotlib (>=3.9.1.post1,<4.0.0)
+Requires-Dist: networkx (>=3.3,<4.0)
+Requires-Dist: numpy (>=1.24,<2.0)
+Requires-Dist: pandas (>=2.2.2,<3.0.0)
+Requires-Dist: plotly (>=6.0.1,<7.0.0)
+Requires-Dist: plotnine (>=0.13.6,<0.14.0)
+Requires-Dist: sankeyflow (>=0.4.1,<0.5.0)
+Requires-Dist: scikit-learn (>=1.5.1,<2.0.0)
+Requires-Dist: seaborn (>=0.13.2,<0.14.0)
+Requires-Dist: tqdm (>=4.66.5,<5.0.0)
+Description-Content-Type: text/markdown
+
+# pyCrossTalkeR
+
+<img src="https://github.com/CostaLab/pyCrossTalkeR/blob/main/logo1.png" align="right" width="200" />
+
+James S. Nagai<sup>1</sup>,
+Nils B. Leimkühler<sup>2</sup>,
+Michael T. Schaub <sup>3</sup>,
+Rebekka K. Schneider<sup>4,5,6</sup>,
+Ivan G. Costa<sup>1*</sup>
+
+<sup>1</sup>Institute for Computational Genomics, Faculty of Medicine, RWTH Aachen University, Aachen, 52074 Germany
+
+<sup>2</sup>Department of Hematology and Stem Cell Transplantation, University Hospital Essen, Germany
+
+<sup>3</sup>Department of Computer Science, RWTH Aachen University, Germany
+
+<sup>4</sup>Department of Cell Biology, Institute for Biomedical Engineering, Faculty of Medicine,RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, NRW, Germany
+
+<sup>5</sup>Oncode Institute, Erasmus Medical Center, Rotterdam, 3015GD, the Netherlands
+
+<sup>6</sup>Department of Hematology, Erasmus Medical Center, Rotterdam, 3015GD, the Netherlands
+
+![Alt text](image.png)
+
+**Motivation:** Ligand-receptor (LR) analysis allows the characterization of cellular crosstalk from single cell RNA-seq data. However, current LR methods provide limited approaches for prioritization of cell types, ligands or receptors or characterizing changes in crosstalk between two biological conditions.
+
+**Results:** pyCrossTalkeR is a framework for network analysis and visualisation of LR networks. pyCrossTalkeR identifies relevant ligands, receptors and cell types contributing to changes in cell communication when contrasting two biological states: disease vs. homeostasis. A case study on scRNA-seq of human myeloproliferative neoplasms reinforces the strengths of pyCrossTalkeR for characterisation of changes in cellular crosstalk in disease state.
+
+## Install
+
+You can install pyCrossTalkeR with the simple commands below:
+
+```{python}
+pip install git+https://github.com/CostaLab/pyCrossTalkeR/
+```
+
+*Note: Please avoid to use the following characters in celltype name: '$'*
+
+## Possible system dependencies
+
+```
+libudunits2-dev
+libgdal-dev
+gdal-bin
+libproj-dev
+proj-data
+proj-bin
+libgeos-dev
+```
+  
+
+## Features v0.0.1
+
+- Single and Comparative Reports
+   - Cell Cell Interaction visualization
+   - Sending and Receiving Cells Ranking
+   - CCI and GCI PCA ranking
+      - All measures and PC table
+      - PC1 and PC2 based barplot
+   - LR pair visualization plot can be done
+
+
+# References
+
+[1] CrossTalkeR: Analysis and Visualisation of Ligand Receptor Networks [link](https://doi.org/10.1093/bioinformatics/btab370)
+
+[2] Heterogeneous bone-marrow stromal progenitors drive myelofibrosis via a druggable alarmin axis. [link](https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(20)30542-7#secsectitle0115)
+
+[3] Comparison of Resources and Methods to infer Cell-Cell Communication from Single-cell RNA Data [link](https://www.biorxiv.org/content/10.1101/2021.05.21.445160v1.full)

pycrosstalker-0.1.0/README.md

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+# pyCrossTalkeR
+
+<img src="https://github.com/CostaLab/pyCrossTalkeR/blob/main/logo1.png" align="right" width="200" />
+
+James S. Nagai<sup>1</sup>,
+Nils B. Leimkühler<sup>2</sup>,
+Michael T. Schaub <sup>3</sup>,
+Rebekka K. Schneider<sup>4,5,6</sup>,
+Ivan G. Costa<sup>1*</sup>
+
+<sup>1</sup>Institute for Computational Genomics, Faculty of Medicine, RWTH Aachen University, Aachen, 52074 Germany
+
+<sup>2</sup>Department of Hematology and Stem Cell Transplantation, University Hospital Essen, Germany
+
+<sup>3</sup>Department of Computer Science, RWTH Aachen University, Germany
+
+<sup>4</sup>Department of Cell Biology, Institute for Biomedical Engineering, Faculty of Medicine,RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, NRW, Germany
+
+<sup>5</sup>Oncode Institute, Erasmus Medical Center, Rotterdam, 3015GD, the Netherlands
+
+<sup>6</sup>Department of Hematology, Erasmus Medical Center, Rotterdam, 3015GD, the Netherlands
+
+![Alt text](image.png)
+
+**Motivation:** Ligand-receptor (LR) analysis allows the characterization of cellular crosstalk from single cell RNA-seq data. However, current LR methods provide limited approaches for prioritization of cell types, ligands or receptors or characterizing changes in crosstalk between two biological conditions.
+
+**Results:** pyCrossTalkeR is a framework for network analysis and visualisation of LR networks. pyCrossTalkeR identifies relevant ligands, receptors and cell types contributing to changes in cell communication when contrasting two biological states: disease vs. homeostasis. A case study on scRNA-seq of human myeloproliferative neoplasms reinforces the strengths of pyCrossTalkeR for characterisation of changes in cellular crosstalk in disease state.
+
+## Install
+
+You can install pyCrossTalkeR with the simple commands below:
+
+```{python}
+pip install git+https://github.com/CostaLab/pyCrossTalkeR/
+```
+
+*Note: Please avoid to use the following characters in celltype name: '$'*
+
+## Possible system dependencies
+
+```
+libudunits2-dev
+libgdal-dev
+gdal-bin
+libproj-dev
+proj-data
+proj-bin
+libgeos-dev
+```
+  
+
+## Features v0.0.1
+
+- Single and Comparative Reports
+   - Cell Cell Interaction visualization
+   - Sending and Receiving Cells Ranking
+   - CCI and GCI PCA ranking
+      - All measures and PC table
+      - PC1 and PC2 based barplot
+   - LR pair visualization plot can be done
+
+
+# References
+
+[1] CrossTalkeR: Analysis and Visualisation of Ligand Receptor Networks [link](https://doi.org/10.1093/bioinformatics/btab370)
+
+[2] Heterogeneous bone-marrow stromal progenitors drive myelofibrosis via a druggable alarmin axis. [link](https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(20)30542-7#secsectitle0115)
+
+[3] Comparison of Resources and Methods to infer Cell-Cell Communication from Single-cell RNA Data [link](https://www.biorxiv.org/content/10.1101/2021.05.21.445160v1.full)

pycrosstalker-0.1.0/pycrosstalker/__init__.py

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+__version__ = "0.0.0.1"
+__author__ = 'James Nagai'
+__credits__ = 'Institute for Computational Genomics'
+
+import pycrosstalker.tools as tl
+import pycrosstalker.plots as pl
+
+
+#Atfan helped to translate some of the code

pycrosstalker-0.1.0/pycrosstalker/plots/__init__.py

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+from .plot import *