sci-epi2gene is designed for Python >=3.6 and requires the following libraries, which will be automatically installed:
| Library | Version | Reference |
|---|---|---|
| NumPy | >= 1.9.0 | Harris, C.R., Millman, K.J., van der Walt, S.J. et al. Array programming with NumPy. Nature 585, 357–362 (2020). DOI: 0.1038/s41586-020-2649-2 |
| tqdm | >= 4.31.0 | 
|
| pandas | >= 1.0.3 | 
|
| sciutil | >= 1.0.3 | 
|
| scibiomart | >= 1.0.1 | 
|
| igv <https://github.com/igvteam/igv-jupyter>_ | >= 0.2.1 | James T. Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P. Mesirov. Integrative Genomics Viewer. Nature Biotechnology 29, 24–26 (2011) |
We strongly encourage you to cite the other python packages
IGV browser was used to generate the image on the first page & if you use the IGV viewer in the notebook please cite IGV.
Data in the tests comes from Encode so if you use any of this data please cite the latest Encode release.
| Library | Version | Reference |
|---|---|---|
| Encode | v107 | https://www.encodeproject.org/help/citing-encode/ |