inferploidy 0.1.1__tar.gz

inferploidy-0.1.1/LICENSE

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+MIT License
+
+Copyright (c) 2023 Seokhyun Yoon
+
+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.

inferploidy-0.1.1/MANIFEST.in

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+include LICENSE
+include README.md
+include requirements.txt
+include src/inferploidy/default_optional_files/*

inferploidy-0.1.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: inferploidy
+Version: 0.1.1
+Summary: Tookits for Tumor cell identification in single-cell RNA-seq data
+Author-email: Seokhyun Yoon <syoon@dku.edu>
+License: MIT License
+        
+        Copyright (c) 2023 Seokhyun Yoon
+        
+        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.
+Project-URL: Homepage, https://github.com/combio-dku
+Keywords: single-cell omics,bioinformatics
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Provides-Extra: dev
+Requires-Dist: numpy; extra == "dev"
+Requires-Dist: pandas; extra == "dev"
+Requires-Dist: scipy; extra == "dev"
+Requires-Dist: scikit-learn; extra == "dev"
+Requires-Dist: scikit-network; extra == "dev"
+Requires-Dist: infercnvpy; extra == "dev"
+Requires-Dist: scanpy; extra == "dev"
+Requires-Dist: seaborn; extra == "dev"
+
+## MLBI_at_DKU_Lib 
+Tookits for Tumor cell identification in single-cell RNA-seq data.
+
+## Contact
+Send email to syoon@dku.edu for any inquiry on the usages.
+

inferploidy-0.1.1/README.md

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+## MLBI_at_DKU_Lib 
+Tookits for Tumor cell identification in single-cell RNA-seq data.
+
+## Contact
+Send email to syoon@dku.edu for any inquiry on the usages.
+

inferploidy-0.1.1/pyproject.toml

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+# pyproject.toml
+
+[build-system]
+requires      = ["setuptools>=61.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "inferploidy"
+version = "0.1.1"
+description = "Tookits for Tumor cell identification in single-cell RNA-seq data"
+readme = "README.md"
+authors = [{ name = "Seokhyun Yoon", email = "syoon@dku.edu" }]
+license = { file = "LICENSE" }
+classifiers = [
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+]
+keywords = ["single-cell omics", "bioinformatics"]
+dependencies = [
+]
+# requires-python = "<3.11"
+
+[project.optional-dependencies]
+dev = ["numpy", "pandas", "scipy", "scikit-learn", "scikit-network", "infercnvpy", "scanpy", "seaborn"]
+
+[project.urls]
+Homepage = "https://github.com/combio-dku"
+
+[project.scripts]
+realpython = "reader.__main__:main"

inferploidy-0.1.1/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

inferploidy-0.1.1/setup.py

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+# setup.py
+
+from setuptools import setup
+
+setup()

inferploidy-0.1.1/src/inferploidy/__init__.py

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+# __init__.py
+# Copyright (c) 2021 (syoon@dku.edu) and contributors
+# https://github.com/combio-dku/MarkerCount/tree/master
+print('https://github.com/combio-dku')
+
+from .inferploidy import run_infercnv, inferploidy
+from .hicat import HiCAT

inferploidy-0.1.1/src/inferploidy/clustering.py

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+import copy, random
+import numpy as np
+import pandas as pd
+import sklearn
+import sklearn.linear_model as lm
+from sklearn.neighbors import kneighbors_graph
+from scipy.sparse import csr_matrix, csc_matrix
+
+CLUSTERING_AGO = 'lv'
+SKNETWORK = True
+try:
+    from sknetwork.clustering import Louvain
+except ImportError:
+    print('WARNING: sknetwork not installed. GMM will be used for clustering.')
+    CLUSTERING_AGO = 'km'
+    SKNETWORK = False
+