We provide installation instructions assuming an Anaconda environment for managing dependencies. Anaconda is a python package/environment manager which can handle complex dependencies between Python packages through the creation of environments. We recommended creating a separate environment for cryodrgn to prevent any conflicts among dependencies with other software packages.

Compute/hardware requirements:

• High performance linux workstation or cluster
• NVIDIA GPUs

Dependencies:

• python
• pytorch
• cudatoolkit
• numpy
• pandas

Additional dependencies for visualization:

• matplotlib
• seaborn
• scipy 1.4.0+
• scikit-learn
• umap
• jupterlab