R package
NestedWGCNA
R package for two-stage gene co-expression analysis.
Coarse-grained module discovery followed by GenFocus-normalized fine-grained module discovery in a nested workflow.
Portfolio
Dai
Personal projects, packages, and tools.
Packages and tools
Current public repositories with documentation where available
R package
uccdf
R package for typed consensus clustering.
Mixed-type data-frame clustering with schema inference, resampling, null testing, supported K selection, and sample-level assignments.
R package
scdown
R package for annotated single-cell RNA-seq downstream analysis.
A narrow package for cluster maps, marker discovery, annotation checks, signature summaries, and ligand-receptor ranking.
R package
cce
R package for counterfactual comparator analysis.
Standardized workflows for survival comparisons, SOC scenario planning, diagnostics, and export contracts in oncology-style analyses.
Python package
litmap
Python package for reproducible literature mapping.
A package and documentation scaffold for explicit run artifacts, cluster mapping, and review-ready literature analysis outputs.
Python package
trait2gene
Python package and CLI for trait-to-gene prioritization.
A PoPS-oriented workflow that standardizes resource resolution, MAGMA handoff, feature preparation, locus prioritization, and reporting.
Python package
turbocellatlas
Python package for atlas-scale single-cell retrieval.
Compressed candidate generation with exact reranking, benchmark artifacts, and documentation for computational and wet-lab users.
Python package
histgraph
Python package for histology-to-spatial-biology modeling.
A pipeline-oriented package for whole-slide histology workflows, graph construction, teacher models, and breast-cancer modeling on compute servers.
Python tool
oncoscape
HPC-oriented spatial pathology scaffold.
A script-first contract for breast cancer spatial workflows, upstream map generation, and downstream biomarker-model handoff.
R package
statsguider
R package for guided statistical test selection.
A narrow workflow that recommends and runs appropriate simple tests from study-design choices in a data frame.
R package
expranno
R package for RNA-seq workflows.
Expression-matrix based workflows for annotation, metadata integration, deconvolution, and signature analysis.
R package
heteff
R package for heterogeneous effect estimation.
Generalized random forest workflows for observational, survival, and instrumental-variable settings.