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Research Areas

Computational BiologySingle-cell, bulk RNA-seq, spatial, and biomarkers
CardiologyCardiovascular signals, cohorts, and interpretationImmunologyImmune cell states, signaling networks, and repertoire dynamicsNeurologyBrain connectivity, functional imaging, and electrophysiologyOncologyTumor microenvironment, immune response, mutations, and survivalPathologyWhole-slide imaging, tissue quantification, and spatial pathology

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Trajectory, spatial, and cohort

The disease_workflows pipeline combines immune trajectory interpretation, spatial niche summaries, and disease cohort comparison.

Trajectory

The pipeline maps immune states onto simple immune axes:

  • naive/memory
  • effector
  • exhausted/terminal
  • B cell maturation
  • myeloid polarization

It also joins clonotypes to pseudotime for lineage tracing summaries.

Spatial

Spatial rows can include x, y, cell type, immune state, and cytokine score. Outputs include:

  • immune niche summaries
  • TLS-like region counts
  • proximity scoring
  • cytokine projection rows
  • spatial pattern classification: inflamed, tolerogenic, suppressive, or mixed

Cohort

Cohort rows can include disease label, disease activity score, medication, timepoint, vaccination/infection history, condition, and response. Outputs include composition proportions, logit proportions, disease presets, and cross-disease deltas.