Wang, D., Hou, S., Zhang, L. et al. iMAP: integration of multiple single-cell datasets by adversarial paired transfer networks. Genome Biol 22, 63 (2021). https://doi.org/10.1186/s13059-021-02280-8
- Install Python >= 3.6. Typically, you should use the Linux system and install a newest version of Anaconda or Miniconda .
- Install pytorch >= 1.1.0. To obtain the optimal performance of deep learning-based models, you should have a Nivdia GPU and install the appropriate version of CUDA. (We tested with CUDA >= 9.0)
- Install scanpy >= 1.6.0 for pre-processing.
- (Optional) Install SHAP for interpretation.
The iMAP python package is available for pip install(pip install imap
). The functions required for the stage I and II of iMAP could be imported from “imap.stage1” and “imap.stage2”, respectively.
Tutorials and API reference are available in the tutorials directory.