[z_Deprecated] Environment set up

To create a clean environment with all the necessary libraries, you can manually install the following packages in a virtual environment (conda recommended) with Python 3.8(.17) and R 4.3:

• Python packages: pandas, numpy, matplotlib, scikit-learn, seaborn, scipy, scikit-bio, rpy2, statsmodels
• R packages:
  • Installable in conda: phyloseq, bindata, tibble, xtable, sva, limma, vegan, MMUPHin, doParallel, dplyr, readr, parallel, ade4, compositions, cqrReg, fastDummies, coda.base
  • Have to individually download:
    • MIDASim
    • FDboost
    • mixOmics

You can potentially set up the environment using conda by executing the following command to create:

conda env create -f env.yml

After this, open R in command line, and then indivudally install the three packages MIDASim, FDboost, and mixOmics from the respective sites linked above.