The Python environment used by zellkonverter for interfacing with the anndata Python library (and H5AD files) is described by the dependencies in .AnnDataDependencies. The zellkonverterAnnDataEnv variable is the basilisk::BasiliskEnvironment() used by zellkonverter.




A character vector containing the pinned versions of all Python packages in zellkonverterAnnDataEnv.

A basilisk::BasiliskEnvironment() containing zellkonverter's AnnData Python environment.


The .AnnDataDependencies variable is exposed for use by other package developers who want an easy way to define the dependencies required for creating a Python environment to work with AnnData objects, most typically within a basilisk context. For example, we can simply combine this vector with additional dependencies to create a basilisk environment with Python package versions that are consistent with those in zellkonverter.

If you want to run code in the exact environment used by zellkonverter this can be done using zellkonverterAnnDataEnv in combination with basilisk::basiliskStart() and/or basilisk::basiliskRun(). Please refer to the basilisk documentation for more information on using these environments.


Luke Zappia

Aaron Lun


#> [1] "anndata==0.7.6"  "h5py==3.2.1"     "hdf5==1.10.6"    "natsort==7.1.1" 
#> [5] "numpy==1.20.2"   "packaging==20.9" "pandas==1.2.4"   "scipy==1.6.3"   
#> [9] "sqlite==3.35.5" 

cl <- basilisk::basiliskStart(zellkonverterAnnDataEnv)
anndata <- reticulate::import("anndata")