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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

Application

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Multi-modal profiling

The multimodal_profiling pipeline supports dependency-gated CITE-seq, ATAC, multiome, and cytometry workflows.

CITE-seq

Tabular ADT inputs are normalized with CLR and summarized with:

  • ADT QC
  • protein heatmap values
  • protein-informed clusters
  • WNN fallback coordinates

ATAC

Tabular peak inputs produce:

  • peak accessibility track rows
  • total accessibility summaries
  • TF motif enrichment cards

Full scATAC preprocessing and peak calling remain gated behind SnapATAC2.

Multiome

The current workflow provides an integration summary using protein clusters and accessible peaks. Full WNN/multiome graph integration remains gated behind muon.

Cytometry

CSV/TSV event tables support:

  • automated lineage marker gating
  • population frequencies
  • cytometry coordinate fallback

Binary FCS parsing remains gated behind FlowUtils or flowutils.