PyOVERCAST 1.0.3__tar.gz → 1.0.4__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {pyovercast-1.0.3 → pyovercast-1.0.4}/PKG-INFO +7 -7
- {pyovercast-1.0.3 → pyovercast-1.0.4}/PyOVERCAST/predict.py +4 -4
- {pyovercast-1.0.3 → pyovercast-1.0.4}/PyOVERCAST.egg-info/PKG-INFO +7 -7
- pyovercast-1.0.4/README.md +46 -0
- {pyovercast-1.0.3 → pyovercast-1.0.4}/pyproject.toml +1 -1
- pyovercast-1.0.3/README.md +0 -46
- {pyovercast-1.0.3 → pyovercast-1.0.4}/LICENSE +0 -0
- {pyovercast-1.0.3 → pyovercast-1.0.4}/PyOVERCAST/__init__.py +0 -0
- {pyovercast-1.0.3 → pyovercast-1.0.4}/PyOVERCAST/clinks.py +0 -0
- {pyovercast-1.0.3 → pyovercast-1.0.4}/PyOVERCAST.egg-info/SOURCES.txt +0 -0
- {pyovercast-1.0.3 → pyovercast-1.0.4}/PyOVERCAST.egg-info/dependency_links.txt +0 -0
- {pyovercast-1.0.3 → pyovercast-1.0.4}/PyOVERCAST.egg-info/entry_points.txt +0 -0
- {pyovercast-1.0.3 → pyovercast-1.0.4}/PyOVERCAST.egg-info/requires.txt +0 -0
- {pyovercast-1.0.3 → pyovercast-1.0.4}/PyOVERCAST.egg-info/top_level.txt +0 -0
- {pyovercast-1.0.3 → pyovercast-1.0.4}/setup.cfg +0 -0
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Metadata-Version: 2.4
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Name: PyOVERCAST
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Version: 1.0.
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Version: 1.0.4
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Summary: A Python package for mining key transcription factors from transcriptome data.
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Author-email: Tinghua Huang <thua45@126.com>
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License-Expression: MIT
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print(sets_names)
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# list avaiable TFs
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tfs_codes = clinks.get_tfs(set_name='
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tfs_codes = clinks.get_tfs(set_name='human_hocomoco_CLink_rci4_1w_0.8')
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print(tfs_codes)
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# get targets
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targets = clinks.get_targets(set_name='
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targets = clinks.get_targets(set_name='human_hocomoco_CLink_rci4_1w_0.8', tf='NFKB1_HUMAN.H11MO.1.B')
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print(targets)
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# predict one DEG-list
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result = predict.olcr(set_names=['
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result = predict.olcr(set_names=['human_jaspar_CLink_rci4_1w_0.8', 'human_hocomoco_CLink_rci4_1w_0.8'], list_file='./PyOVERCAST_data/input_deg-list.txt', win=30, thread_n=16)
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# or predict one DEG-list with bootstrap
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result = predict.olcr_bootstrap(set_names=['
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result = predict.olcr_bootstrap(set_names=['human_jaspar_CLink_rci4_1w_0.8', 'human_hocomoco_CLink_rci4_1w_0.8'], list_file='./OVERCAST_data/input_deg-list.txt', win=30, bs_n=1000, thread_n=32)
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# save result to text file
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result.to_csv('output.txt', sep='\t', index=False, encoding='utf-8')
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# plot OLC matrix
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predict.plot_olc(set_names=['
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predict.plot_olc(set_names=['human_jaspar_CLink_rci4_1w_0.8', 'human_hocomoco_CLink_rci4_1w_0.8'], list_file='./PyOVERCAST_data/input_deg-list.txt', tf='MA0844.2_XBP1', win=30)
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# plot fitted 3D U-surface
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predict.plot_fit3D(set_names=['
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predict.plot_fit3D(set_names=['human_jaspar_CLink_rci4_1w_0.8', 'human_hocomoco_CLink_rci4_1w_0.8'], list_file='./PyOVERCAST_data/input_deg-list.txt', tf='MA0844.2_XBP1', win=30)
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```
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if __name__ == '__main__':
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'''
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result = olcr(set_names=['
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result = olcr(set_names=['human_jaspar_CLink_rci4_1w_0.8', 'human_hocomoco_CLink_rci4_1w_0.8'], list_file='OVERCAST_data/input_deg-list.txt', win=30, thread_n=16)
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result.to_csv('output.txt', sep='\t', index=False, encoding='utf-8')
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result = olcr_bootstrap(set_names=['
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result = olcr_bootstrap(set_names=['human_jaspar_CLink_rci4_1w_0.8', 'human_hocomoco_CLink_rci4_1w_0.8'], list_file='OVERCAST_data/input_deg-list.txt', win=30, thread_n=16)
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result.to_csv('output_bootstrap.txt', sep='\t', index=False, encoding='utf-8')
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'''
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#plot_olc(set_names=['
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#plot_olc(set_names=['human_jaspar_CLink_rci4_1w_0.8', 'human_hocomoco_CLink_rci4_1w_0.8'], list_file='OVERCAST_data/input_deg-list.txt', tf='MA0844.2_XBP1', win=30)
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#plot_fit3D(set_names=['
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#plot_fit3D(set_names=['human_jaspar_CLink_rci4_1w_0.8', 'human_hocomoco_CLink_rci4_1w_0.8'], list_file='OVERCAST_data/input_deg-list.txt', tf='MA0844.2_XBP1', win=30)
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Metadata-Version: 2.4
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Name: PyOVERCAST
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Version: 1.0.
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Version: 1.0.4
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Summary: A Python package for mining key transcription factors from transcriptome data.
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Author-email: Tinghua Huang <thua45@126.com>
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License-Expression: MIT
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print(sets_names)
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# list avaiable TFs
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tfs_codes = clinks.get_tfs(set_name='
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tfs_codes = clinks.get_tfs(set_name='human_hocomoco_CLink_rci4_1w_0.8')
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print(tfs_codes)
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# get targets
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targets = clinks.get_targets(set_name='
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targets = clinks.get_targets(set_name='human_hocomoco_CLink_rci4_1w_0.8', tf='NFKB1_HUMAN.H11MO.1.B')
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print(targets)
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# predict one DEG-list
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result = predict.olcr(set_names=['
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result = predict.olcr(set_names=['human_jaspar_CLink_rci4_1w_0.8', 'human_hocomoco_CLink_rci4_1w_0.8'], list_file='./PyOVERCAST_data/input_deg-list.txt', win=30, thread_n=16)
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# or predict one DEG-list with bootstrap
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result = predict.olcr_bootstrap(set_names=['
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result = predict.olcr_bootstrap(set_names=['human_jaspar_CLink_rci4_1w_0.8', 'human_hocomoco_CLink_rci4_1w_0.8'], list_file='./OVERCAST_data/input_deg-list.txt', win=30, bs_n=1000, thread_n=32)
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# save result to text file
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result.to_csv('output.txt', sep='\t', index=False, encoding='utf-8')
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# plot OLC matrix
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predict.plot_olc(set_names=['
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predict.plot_olc(set_names=['human_jaspar_CLink_rci4_1w_0.8', 'human_hocomoco_CLink_rci4_1w_0.8'], list_file='./PyOVERCAST_data/input_deg-list.txt', tf='MA0844.2_XBP1', win=30)
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# plot fitted 3D U-surface
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predict.plot_fit3D(set_names=['
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predict.plot_fit3D(set_names=['human_jaspar_CLink_rci4_1w_0.8', 'human_hocomoco_CLink_rci4_1w_0.8'], list_file='./PyOVERCAST_data/input_deg-list.txt', tf='MA0844.2_XBP1', win=30)
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```
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# PyOVERCAST
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A Python package for mining key transcription factors from transcriptome data.
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## Installation
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```bash
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pip install numpy pandas statsmodels scipy seaborn matplotlib PyOVERCAST
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```
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## Usage
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```python
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from PyOVERCAST import clinks, predict
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if __name__ == '__main__':
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# download TF-target set, only need to run once!!!
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clinks.download_data()
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# list available TF-target set
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sets_names = clinks.get_sets(species='Homo sapiens')
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print(sets_names)
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# list avaiable TFs
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tfs_codes = clinks.get_tfs(set_name='human_hocomoco_CLink_rci4_1w_0.8')
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print(tfs_codes)
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# get targets
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targets = clinks.get_targets(set_name='human_hocomoco_CLink_rci4_1w_0.8', tf='NFKB1_HUMAN.H11MO.1.B')
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print(targets)
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# predict one DEG-list
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result = predict.olcr(set_names=['human_jaspar_CLink_rci4_1w_0.8', 'human_hocomoco_CLink_rci4_1w_0.8'], list_file='./PyOVERCAST_data/input_deg-list.txt', win=30, thread_n=16)
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# or predict one DEG-list with bootstrap
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result = predict.olcr_bootstrap(set_names=['human_jaspar_CLink_rci4_1w_0.8', 'human_hocomoco_CLink_rci4_1w_0.8'], list_file='./OVERCAST_data/input_deg-list.txt', win=30, bs_n=1000, thread_n=32)
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# save result to text file
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result.to_csv('output.txt', sep='\t', index=False, encoding='utf-8')
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# plot OLC matrix
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predict.plot_olc(set_names=['human_jaspar_CLink_rci4_1w_0.8', 'human_hocomoco_CLink_rci4_1w_0.8'], list_file='./PyOVERCAST_data/input_deg-list.txt', tf='MA0844.2_XBP1', win=30)
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# plot fitted 3D U-surface
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predict.plot_fit3D(set_names=['human_jaspar_CLink_rci4_1w_0.8', 'human_hocomoco_CLink_rci4_1w_0.8'], list_file='./PyOVERCAST_data/input_deg-list.txt', tf='MA0844.2_XBP1', win=30)
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```
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[project]
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name = "PyOVERCAST"
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version = "1.0.
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version = "1.0.4"
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license = "MIT" # SPDX expression
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description = "A Python package for mining key transcription factors from transcriptome data."
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readme = "README.md"
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pyovercast-1.0.3/README.md
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# PyOVERCAST
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A Python package for mining key transcription factors from transcriptome data.
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## Installation
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```bash
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pip install numpy pandas statsmodels scipy seaborn matplotlib PyOVERCAST
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```
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## Usage
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```python
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from PyOVERCAST import clinks, predict
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if __name__ == '__main__':
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# download TF-target set, only need to run once!!!
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clinks.download_data()
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# list available TF-target set
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sets_names = clinks.get_sets(species='Homo sapiens')
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print(sets_names)
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# list avaiable TFs
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tfs_codes = clinks.get_tfs(set_name='human_hocomoco_CLink_wtcoor_1w_0.8')
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print(tfs_codes)
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# get targets
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targets = clinks.get_targets(set_name='human_hocomoco_CLink_wtcoor_1w_0.8', tf='NFKB1_HUMAN.H11MO.1.B')
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print(targets)
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# predict one DEG-list
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result = predict.olcr(set_names=['human_hocomoco_CLink_wtcoor_1w_0.8', 'human_jaspar_CLink_wtcoor_1w_0.8'], list_file='./PyOVERCAST_data/input_deg-list.txt', win=30, thread_n=16)
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# or predict one DEG-list with bootstrap
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result = predict.olcr_bootstrap(set_names=['human_hocomoco_CLink_wtcoor_1w_0.8', 'human_jaspar_CLink_wtcoor_1w_0.8'], list_file='./OVERCAST_data/input_deg-list.txt', win=30, bs_n=1000, thread_n=32)
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# save result to text file
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result.to_csv('output.txt', sep='\t', index=False, encoding='utf-8')
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# plot OLC matrix
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predict.plot_olc(set_names=['human_hocomoco_CLink_wtcoor_1w_0.8', 'human_jaspar_CLink_wtcoor_1w_0.8'], list_file='./PyOVERCAST_data/input_deg-list.txt', tf='MA0844.2_XBP1', win=30)
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# plot fitted 3D U-surface
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predict.plot_fit3D(set_names=['human_hocomoco_CLink_wtcoor_1w_0.8', 'human_jaspar_CLink_wtcoor_1w_0.8'], list_file='./PyOVERCAST_data/input_deg-list.txt', tf='MA0844.2_XBP1', win=30)
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```
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