camaralab/python3 repository overview

These are mostly based on the jupyter/tensorflow-notebook or jupyter/datascience-notebook Docker images. They usually contain Python version 3.6.5.

Run using:

docker run -it -p 8888:8888 -v "/e/Dropbox (Camara Lab)/Camara Lab's shared workspace:/home/jovyan/Dropbox" -e GRANT_SUDO=yes --user root camaralab/python3:scVI

Tags:

ot - dependencies installed for CAJAL (but not CAJAL installed)

microns - packages for downloading and plotting triangular meshes from MICrONS (meshparty, trimesh, etc)

spharm - SPHARM (https://github.com/applied-systems-biology/Dynamic_SPHARM⁠) and dependencies

cellphonedb - CellPhoneDB and dependencies

gudhi - GUDHI (python package for topological data analysis) and dependencies

scVI & scVI_v2 - different versions of scVI and dependencies

esmfold: requires local installation of CUDA 11.6 (esmfold requires openfold, which uses pytorch 1.12, which only supports up to CUDA 11.6). Please also check for compatible GPU hardware