beta_vae_lnclassifier/environment.yml at master · cbib/beta_vae_lnclassifier · GitHub

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name: beta_lncrna
channels:
  - pytorch
  - nvidia
  - conda-forge

dependencies:
  # Python
  - python=3.10

  # PyTorch with CUDA
  - pytorch::pytorch=2.5.1
  - pytorch::torchvision=0.20.1
  - pytorch::torchaudio=2.5.1
  - pytorch::pytorch-cuda=12.1
  - pytorch::pytorch-mutex=1.0=cuda

  # Core scientific computing
  - numpy=1.26.4
  - pandas=2.3.3
  - scipy=1.15.3

  # Machine learning
  - scikit-learn=1.6.1
  - scikit-image=0.25.2

  # Bioinformatics
  - biopython=1.85

  # Visualization
  - matplotlib=3.10.3
  - seaborn=0.13.2
  - upsetplot=0.9.0

  # HDF5 support
  - h5py=3.15.1
  - pytables=3.10.1

  # Utilities
  - pyyaml=6.0.2
  - tqdm=4.67.1
  - joblib=1.5.1

  # Statistical analysis
  - statsmodels=0.14.6

  # Development
  - jupyter
  - jupyterlab
  - ipython

  # From pip (contains lncRNABERT specific packages)
  - pip
  - pip:
      - sentencepiece==0.2.0
      - tqdm==4.67.0
      - umap-learn==0.5.7
      - numba==0.60.0
      - llvmlite==0.43.0