In order to run the analysis notebooks, a different environment is needed for setup. Described below. In addition, the user needs to install R on their own machine separate from the conda env. The following commands/packages needs to be run/installed:
- install.packages("devtools")
- devtools::install_github("b0rxa/scmamp")
Due to version issues and function depreciations, I made a few changes to the analysis_helper file that fixes some of the conversions that were depreciated in newer versions of rpy2.
We also need to add in the cached files from the different experiments (mainly experiment 3 [the bench marking]) so that the analysis notebooks can be run without needing the full results.
Conda Environment:
name: rpy2-env
channels:
- defaults
dependencies:
- python=3.12
- rpy2
- jupyter
- pandas
- numpy
- pip:
- statsmodels
- pingouin
- seaborn
In order to run the analysis notebooks, a different environment is needed for setup. Described below. In addition, the user needs to install R on their own machine separate from the conda env. The following commands/packages needs to be run/installed:
Due to version issues and function depreciations, I made a few changes to the analysis_helper file that fixes some of the conversions that were depreciated in newer versions of rpy2.
We also need to add in the cached files from the different experiments (mainly experiment 3 [the bench marking]) so that the analysis notebooks can be run without needing the full results.
Conda Environment:
name: rpy2-env
channels:
dependencies: