PyOVERCAST
A Python package for mining key transcription factors from transcriptome data.
Installation
pip install numpy pandas statsmodels scipy seaborn matplotlib PyOVERCAST
Usage
from PyOVERCAST import clinks, predict
if __name__ == '__main__':
# download TF-target set, only need to run once!!!
clinks.download_data()
# list available TF-target set
sets_names = clinks.get_sets(species='Homo sapiens')
print(sets_names)
# list avaiable TFs
tfs_codes = clinks.get_tfs(set_name='human_hocomoco_CLink_rci4_1w_0.8')
print(tfs_codes)
# get targets
targets = clinks.get_targets(set_name='human_hocomoco_CLink_rci4_1w_0.8', tf='NFKB1_HUMAN.H11MO.1.B')
print(targets)
# predict one DEG-list
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)
# or predict one DEG-list with bootstrap
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)
# save result to text file
result.to_csv('output.txt', sep='\t', index=False, encoding='utf-8')
# plot OLC matrix
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)
# plot OLC matrix
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)
# plot fitted 3D U-surface
predict.plot_contour(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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Release files for PyOVERCAST 1.0.8
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| pyovercast-1.0.8.tar.gz | 13.1 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| pyovercast-1.0.8-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 25.8 kB
Release files / pyovercast-1.0.8.tar.gz
| Download URL | pyovercast-1.0.8.tar.gz |
|---|---|
| Size | 13.1 kB |
| Tags | Source |
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Release files / pyovercast-1.0.8-py3-none-any.whl
| Download URL | pyovercast-1.0.8-py3-none-any.whl |
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| Size | 12.7 kB |
| Tags | Python 3 |
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