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cyCombinePy 0.1.2
cyCombinePy 0.1.2

Getting started

  • Installation
  • Usage guide
  • Citation

Tutorials

  • Main cyCombine workflow (Python port)
  • Detecting batch effects (Python port)
  • CITE-seq ADT batch correction benchmark

Reference

  • API reference
    • cycombinepy.transform_asinh
    • cycombinepy.normalize
    • cycombinepy.create_som
    • cycombinepy.batch_correct
    • cycombinepy.correct_data
    • cycombinepy.CombatCorrectionError
    • cycombinepy.ConfoundedDesignError
    • cycombinepy.correct.CORRECTED_LAYER
    • cycombinepy.correct.CORRECTION_REPORT_UNS_KEY
    • cycombinepy.correct.CORRECTION_REPORT_SCHEMA_VERSION
    • cycombinepy.compute_emd
    • cycombinepy.evaluate_emd
    • cycombinepy.compute_mad
    • cycombinepy.evaluate_mad
    • cycombinepy.detect_batch_effect
    • cycombinepy.detect_batch_effect_express
    • cycombinepy.get_markers
    • cycombinepy.check_confound
    • cycombinepy.io.read_fcs_dir
    • cycombinepy.plotting.plot_density
    • cycombinepy.plotting.plot_dimred
    • cycombinepy.plotting.plot_emd_heatmap
    • cycombinepy.evaluate.scib_metrics
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