AlphaMicrobiome 0.1.0__tar.gz

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Files changed (21) hide show
  1. alphamicrobiome-0.1.0/PKG-INFO +25 -0
  2. alphamicrobiome-0.1.0/pyproject.toml +42 -0
  3. alphamicrobiome-0.1.0/setup.cfg +4 -0
  4. alphamicrobiome-0.1.0/src/AlphaMicrobiome.egg-info/PKG-INFO +25 -0
  5. alphamicrobiome-0.1.0/src/AlphaMicrobiome.egg-info/SOURCES.txt +19 -0
  6. alphamicrobiome-0.1.0/src/AlphaMicrobiome.egg-info/dependency_links.txt +1 -0
  7. alphamicrobiome-0.1.0/src/AlphaMicrobiome.egg-info/requires.txt +18 -0
  8. alphamicrobiome-0.1.0/src/AlphaMicrobiome.egg-info/top_level.txt +1 -0
  9. alphamicrobiome-0.1.0/src/microbiome/__init__.py +24 -0
  10. alphamicrobiome-0.1.0/src/microbiome/amplicon.py +582 -0
  11. alphamicrobiome-0.1.0/src/microbiome/betaNTI.py +792 -0
  12. alphamicrobiome-0.1.0/src/microbiome/colors.py +122 -0
  13. alphamicrobiome-0.1.0/src/microbiome/diversity.py +222 -0
  14. alphamicrobiome-0.1.0/src/microbiome/journal.py +54 -0
  15. alphamicrobiome-0.1.0/src/microbiome/metacyc_utils.py +86 -0
  16. alphamicrobiome-0.1.0/src/microbiome/network.py +838 -0
  17. alphamicrobiome-0.1.0/src/microbiome/plot.py +54 -0
  18. alphamicrobiome-0.1.0/src/microbiome/skbio_utils.py +220 -0
  19. alphamicrobiome-0.1.0/src/microbiome/stats.py +171 -0
  20. alphamicrobiome-0.1.0/src/microbiome/usearch.py +256 -0
  21. alphamicrobiome-0.1.0/src/microbiome/vae.py +438 -0
alphamicrobiome-0.1.0/PKG-INFO ADDED
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+ Metadata-Version: 2.4
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+ Name: AlphaMicrobiome
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+ Version: 0.1.0
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+ Summary: Microbiome analysis
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+ Author: Zhao Yu
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+ Requires-Python: >=3.12
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+ Description-Content-Type: text/markdown
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+ Requires-Dist: ipykernel
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+ Requires-Dist: loguru
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+ Requires-Dist: tqdm
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+ Requires-Dist: numpy
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+ Requires-Dist: pandas
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+ Requires-Dist: scipy
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+ Requires-Dist: statsmodels
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+ Requires-Dist: pingouin
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+ Requires-Dist: matplotlib
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+ Requires-Dist: seaborn
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+ Requires-Dist: statannotations
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+ Requires-Dist: scikit-learn
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+ Requires-Dist: shap
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+ Requires-Dist: torch
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+ Requires-Dist: torchvision
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+ Requires-Dist: scikit-bio
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+ Requires-Dist: networkx
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+ Requires-Dist: reflex
alphamicrobiome-0.1.0/pyproject.toml ADDED
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+ [project]
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+ name = "AlphaMicrobiome"
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+ version = "0.1.0"
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+ description = "Microbiome analysis"
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+ authors = [
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+ {name='Zhao Yu'}
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+ ]
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+ readme = "README.md"
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+ requires-python = ">=3.12"
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+ dependencies = [
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+ # kernel for Jupyter notebooks
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+ 'ipykernel',
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+ 'loguru',
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+ 'tqdm',
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+ # Scientific computing and visualization
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+ 'numpy',
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+ 'pandas',
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+ 'scipy',
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+ 'statsmodels',
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+ 'pingouin',
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+ 'matplotlib',
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+ 'seaborn',
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+ 'statannotations',
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+ # ML and DL
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+ 'scikit-learn',
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+ 'shap',
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+ 'torch',
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+ 'torchvision',
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+ # Microbiome analysis
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+ 'scikit-bio',
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+ # 'lefse',
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+ 'networkx',
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+ # Web
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+ 'reflex',
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+ ]
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+
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+ [build-system]
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+ requires = ["setuptools", "wheel"]
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+ build-backend = "setuptools.build_meta"
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+
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+ [tool.setuptools.packages.find]
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+ where = ["src"]
alphamicrobiome-0.1.0/setup.cfg ADDED
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+ [egg_info]
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+ tag_build =
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+ tag_date = 0
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+
alphamicrobiome-0.1.0/src/AlphaMicrobiome.egg-info/PKG-INFO ADDED
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+ Metadata-Version: 2.4
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+ Name: AlphaMicrobiome
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+ Version: 0.1.0
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+ Summary: Microbiome analysis
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+ Author: Zhao Yu
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+ Requires-Python: >=3.12
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+ Description-Content-Type: text/markdown
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+ Requires-Dist: ipykernel
9
+ Requires-Dist: loguru
10
+ Requires-Dist: tqdm
11
+ Requires-Dist: numpy
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+ Requires-Dist: pandas
13
+ Requires-Dist: scipy
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+ Requires-Dist: statsmodels
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+ Requires-Dist: pingouin
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+ Requires-Dist: matplotlib
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+ Requires-Dist: seaborn
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+ Requires-Dist: statannotations
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+ Requires-Dist: scikit-learn
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+ Requires-Dist: shap
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+ Requires-Dist: torch
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+ Requires-Dist: torchvision
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+ Requires-Dist: scikit-bio
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+ Requires-Dist: networkx
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+ Requires-Dist: reflex
alphamicrobiome-0.1.0/src/AlphaMicrobiome.egg-info/SOURCES.txt ADDED
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+ pyproject.toml
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+ src/AlphaMicrobiome.egg-info/PKG-INFO
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+ src/AlphaMicrobiome.egg-info/SOURCES.txt
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+ src/AlphaMicrobiome.egg-info/dependency_links.txt
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+ src/AlphaMicrobiome.egg-info/requires.txt
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+ src/AlphaMicrobiome.egg-info/top_level.txt
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+ src/microbiome/__init__.py
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+ src/microbiome/amplicon.py
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+ src/microbiome/betaNTI.py
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+ src/microbiome/colors.py
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+ src/microbiome/diversity.py
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+ src/microbiome/journal.py
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+ src/microbiome/metacyc_utils.py
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+ src/microbiome/network.py
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+ src/microbiome/plot.py
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+ src/microbiome/skbio_utils.py
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+ src/microbiome/stats.py
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+ src/microbiome/usearch.py
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+ src/microbiome/vae.py
alphamicrobiome-0.1.0/src/AlphaMicrobiome.egg-info/requires.txt ADDED
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+ ipykernel
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+ loguru
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+ tqdm
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+ numpy
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+ pandas
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+ scipy
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+ statsmodels
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+ pingouin
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+ matplotlib
10
+ seaborn
11
+ statannotations
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+ scikit-learn
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+ shap
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+ torch
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+ torchvision
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+ scikit-bio
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+ networkx
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+ reflex
alphamicrobiome-0.1.0/src/microbiome/__init__.py ADDED
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+
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+
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+ from . import (
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+ amplicon,
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+ diversity,
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+ network,
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+ vae,
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+ stats,
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+ colors,
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+ plot,
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+ )
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+
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+ __version__ = "0.1.0"
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+ __author__ = "ZhaoYu"
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+ __all__ = [
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+ 'amplicon',
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+ 'diversity',
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+ 'network',
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+ 'vae',
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+ 'stats',
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+ 'betaNTI',
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+ 'colors',
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+ 'plot',
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+ ]