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scArches documentation
scArches documentation

Main

  • scArches (PyTorch) - single-cell architecture surgery
  • Installation
  • API
    • Data Processing
    • Models
    • Plotting
    • Utils
    • Zenodo
  • A few tips on training models

Examples

  • Unsupervised surgery pipeline with SCVI
  • Semi-supervised surgery pipeline with SCANVI
  • Multi-Modal Surgery Pipeline with TOTALVI
  • Unsupervised surgery pipeline with TRVAE
  • Build reference atlas from scratch
  • Reference maping using scGen
  • Basic tutorial for query to reference maping using expiMap
  • Advanced tutorial for query to reference mapping using expiMap with de novo learned gene programs
  • treeArches: learning and updating a cell-type hierarchy (basic tutorial)
  • treeArches: identifying new cell types (advanced tutorial)
  • Spatial reconstruction of the mouse embryo with SageNet
  • Tutorial for mvTCR
  • Integration and reference mapping with multigrate
  • Integration, label transfer and multi-scale analysis with scPoli
  • Integration of scATAC data with scPoli
  • Mapping data to the Human Lung Cell Atlas for joint analysis and cell type label transfer
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Copyright © 2025, Mohammad Lotfollahi, Sergei Rybakov, Mohsen Naghipourfar
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