AnnData-Environment {zellkonverter} | R Documentation

## AnnData environment

### Description

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.

### Usage

    .AnnDataDependencies

    zellkonverterAnnDataEnv

### Format

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

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

### Details

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.

### Author(s)

Luke Zappia

Aaron Lun

### Examples

    .AnnDataDependencies

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

[Package zellkonverter version 1.2.1 Index]