tangermeme

Getting Started

  • tangermeme
  • Release History

Operations

  • Tutorial A1: Sequence Manipulation
  • Tutorial A2: Predictions
  • Tutorial A3: DeepLIFT/SHAP
  • Tutorial A4: Seqlets
  • Tutorial A5: Annotations
  • Tutorial B1: Marginalization
  • Tutorial B2: Ablation
  • Tutorial B3: Spacing
  • Tutorial B4: In Silico Saturation Mutagenesis (ISM)
  • Tutorial B5: Variant Effect
  • Tutorial B6: Design
  • Greedy Saturation Mutagenesis / Evolutionary Algorithms
  • Designing Constructs
  • Tutorial B7: Cartesian Product
  • Tutorial C1: I/O and Data Loading
  • Tutorial C2: Plotting

How To

  • How To: Reduce Friction and Save Time with Tangermeme

Vignettes

  • Attribution Trickiness and DeepLiftShap Implementations
  • Inspecting what Cis-Regulatory Features a Model Has Learned
  • Wrappers are Producitvity Hacks
  • Conclusions

Paper Notebooks

  • Initial Demonstrations of Tangermeme
  • Seqlet Calling and Downstream Analyses

API

  • ablate
  • annotate
  • design
  • ersatz
  • io
  • ism
  • marginalize
  • match
  • predict
  • product
  • seqlet
  • space
  • utils
  • variant_effect
tangermeme
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