tikhonov-cli

Standalone CLI for Harmony2 single-cell integration. Reads an .h5ad file, runs Harmony2 on a PC embedding, writes the corrected embedding back, and emits Patikas-schema benchmark JSON.

Install

cargo install tikhonov-cli

This installs the tikhonov binary.

Quickstart

tikhonov \
  --input data.h5ad \
  --pc-key X_pca \
  --covariate-factors sample \
  --output-key X_harmony \
  --iterations 10 \
  --num-pcs 20 \
  --num-clusters 50 \
  --sigma 0.1 \
  --theta 2.0 \
  --ncpus 16 \
  --bench-json results/run.json

The corrected embedding lands in obsm["X_harmony"] of the input file.

Patikas benchmark reproduction

The flag set matches Patikas et al. 2026's RunHarmony.R with one addition (--input <path>). Emitted JSON matches the schema at harmony2-ms/tahoe/benchmark/results/, so our results drop into their notebook unchanged.

HDF5 dependency

This crate links against libhdf5. On Fedora: dnf install hdf5-devel. On macOS: brew install hdf5. On Ubuntu: apt install libhdf5-dev. Static builds are available via hdf5-metno's static feature at the cost of longer compile times.

License

Apache-2.0.