modamix 0.0.1__tar.gz

modamix-0.0.1/LICENSE

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+MIT License
+
+Copyright (c) 2025 cbi-bioinfo
+
+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.

modamix-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: modamix
+Version: 0.0.1
+Summary: A Unified Framework for Correcting Batch Effects and Integrating Multi-Omics Data
+Home-page: https://github.com/cbi-bioinfo/MoDAmix
+Author: miniymay
+Author-email: joungmin@vt.edu
+Keywords: modamix
+Classifier: Programming Language :: Python :: 3.6
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Requires-Python: >=3.6
+License-File: LICENSE
+Requires-Dist: torch
+Requires-Dist: pandas
+Requires-Dist: os
+Requires-Dist: numpy
+Requires-Dist: sys
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary

modamix-0.0.1/README.md

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+# MoDAmix
+A Unified Framework for Correcting Batch Effects and Integrating Multi-Omics Data
+
+## Requirements
+* Python (>= 3.6)
+* Pytorch (>= v1.6.0)
+* Other python packages : numpy (>=1.19.1), pandas (>=1.1.1), os, sys, random
+
+## Usage
+Clone the repository or download source code files.
+
+## Inputs
+[Note!] All the example datasets can be found in './example_data/' directory.
+
+### 1. Source multi-omics dataset
+* First omics profiles to be used as source domain (**Source_omics1_X, Source_omics2_X**)
+  - Row : Sample, Column : Feature
+  - The first column should have "sample id", and the first row should contain the feature names
+  - Samples should be sorted in the same order for both omics 1 and omics 2 profiles
+  - Example : ./example_data/source_omics1_example_X.csv, source_omics12_example_X.csv
+* Integer-converted subtype label for the source dataset (**Source_Y**)
+  - The column name should be "subtype", and the rows should be sorted in the same way as the ones in "Source_omics1_X".
+  - The subtype label should start from 0
+  - Example : ./example_data/source_example_y.csv
+
+### 2. Target multi-omics dataset
+* Unlabeled multi-omics profiles to be used as target domain (**Target_omics1_X, Target_omics2_X**)
+   - Row : Sample, Column : Feature 
+   - The first column should have "sample_id" and the last two coulmns shoud be "batch" and "domain_idx" which contain the batch name (string) and integer number (index) discriminating each dataset. Samples in the same dataset should have same number and "domain_idx" should start from 1. You can have multiple batch inside.
+   - The first row should contain the feature names.
+   - Samples should be sorted in the same order for both omics 1 and omics 2 profiles and batch number should be also same for both omics profiles. For example, if you set "batch_A" as 1 for "domain_idx" in omics 1 profiles, then "batch_A" should have same number 1 as "domian_idx" in omics 2 profiles.
+   - Example : ./example_data/target_omics1_example_X.csv, target_omics2_example_X.csv
+ 
+### 3. Meta data
+* Category information
+  - This information will be used to convert each integer subtype label with the acutual category name (e.g., cell type, cancer subtype) and provide the prediction result for targe dataset.
+  - This file should have two columns named with "subtype" and "subtype_int", which indicate the actual subtype name and the integer-converted subtype label you provided in "Source_Y".
+  - Example : ./example_data/subtype_category_info.csv
+ 
+* Batch information
+  - This information will be used to convert each batch integer index with the acutual batch name and provide the prediction result for targe dataset.
+  - This file should have two columns named with "batch" and "domain_idx", which indicate the actual batch name and the integer-converted batch index you provided in "Target_omics1_X".
+  - Example : ./example_data/batch_category_info.csv
+ 
+## How to run (Example)
+1. Clone the respository, move to the cloned directory, and edit the **run_MoDAmix.sh** to make sure each variable indicate the corresponding files.
+2. Run the below command :
+```
+chmod +x run_MoDAmix.sh
+./run_MoDAmix.sh
+```
+If you clone the directory and run the above command directly, you will get the result for the example dataset.
+
+3. All the results will be saved in the newly created **results** directory.
+   * batch_corrected features.csv : multi-omics integrated batch corrected features for both source and target dataset
+   * results_target_prediction.csv : predicted subtype label for each sample in target dataset
+
+## Contact
+If you have any questions or problems, please contact to joungmin AT vt.edu

modamix-0.0.1/modamix.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: modamix
+Version: 0.0.1
+Summary: A Unified Framework for Correcting Batch Effects and Integrating Multi-Omics Data
+Home-page: https://github.com/cbi-bioinfo/MoDAmix
+Author: miniymay
+Author-email: joungmin@vt.edu
+Keywords: modamix
+Classifier: Programming Language :: Python :: 3.6
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Requires-Python: >=3.6
+License-File: LICENSE
+Requires-Dist: torch
+Requires-Dist: pandas
+Requires-Dist: os
+Requires-Dist: numpy
+Requires-Dist: sys
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary

modamix-0.0.1/modamix.egg-info/SOURCES.txt

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+LICENSE
+README.md
+setup.py
+modamix.egg-info/PKG-INFO
+modamix.egg-info/SOURCES.txt
+modamix.egg-info/dependency_links.txt
+modamix.egg-info/not-zip-safe
+modamix.egg-info/requires.txt
+modamix.egg-info/top_level.txt

modamix-0.0.1/modamix.egg-info/dependency_links.txt

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+

modamix-0.0.1/modamix.egg-info/not-zip-safe

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+

modamix-0.0.1/modamix.egg-info/requires.txt

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+torch
+pandas
+os
+numpy
+sys

modamix-0.0.1/modamix.egg-info/top_level.txt

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+

modamix-0.0.1/setup.cfg

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

modamix-0.0.1/setup.py

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+from setuptools import setup, find_packages
+
+setup(
+    name='modamix',
+    version='0.0.1',
+    description='A Unified Framework for Correcting Batch Effects and Integrating Multi-Omics Data',
+    author='miniymay',
+    author_email='joungmin@vt.edu',
+    url='https://github.com/cbi-bioinfo/MoDAmix',
+    install_requires=['torch', 'pandas', 'os', 'numpy', 'sys',],
+    packages=find_packages(exclude=[]),
+    keywords=['modamix'],
+    python_requires='>=3.6',
+    package_data={},
+    zip_safe=False,
+    classifiers=[
+        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7',
+        'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
+    ],
+)