Welcome to MIDAS’s documentation!

MIDAS turns mosaic data into imputed and batch-corrected data to support single-cell multimodal analysis.

Contents:

• Installation
  • Step 1: Create a New Environment
  • Step 2: Install scmidas
• Tutorials
  • Basics
    • Inputs of MIDAS
    • Outputs of MIDAS
    • Rectangular Integration of RNA+ADT
    • Mosaic Integration of RNA+ADT
    • Mosaic Integration of RNA+ADT+ATAC
  • Advanced
    • Visualizing the Training Process (TensorBoard)
    • Training with Multi-GPU
    • Development Instructions
• API
  • scmidas.config
    • load_config()
  • scmidas.model
    • Decoder
    • Discriminator
    • Encoder
    • MIDAS
    • S_Decoder
    • S_Encoder
    • VAE
  • scmidas.data
    • BasicModDataset
    • MatDataset
    • MultiBatchSampler
    • MultiModalDataset
    • MyDistributedSampler
    • VecDataset
    • download_data()
    • download_file()
    • unzip_file()
  • scmidas.nn
    • ActivationRegistry
    • DistributionRegistry
    • Layer1D
    • MLP
    • TransformRegistry
  • scmidas.utils
    • convert_tensor_to_list()
    • convert_tensors_to_cuda()
    • detach_tensors()
    • exp()
    • extract_params()
    • extract_values()
    • filter_keys()
    • generate_all_combinations()
    • get_filenames()
    • get_name_fmt()
    • get_pred_dirs()
    • get_s_joint_mods()
    • load_csv()
    • load_predicted()
    • log()
    • mkdir()
    • mkdirs()
    • ref_sort()
    • reverse_dict()
    • reverse_trsf()
    • rmdir()
    • save_list_to_csv()
    • save_tensor_to_csv()
• Release notes
  • v0.1.0 2024-12-20
  • v0.0.18 2024-07-29
  • v0.0.17 2024-07-16
  • v0.0.16 2024-07-11
  • v0.0.15 2024-07-11
  • v0.0.14 2024-07-04
  • v0.0.13 2024-07-04
  • v0.0.8 2024-06-20