SPARC CCF Multi-omics analysis
A pipeline to predict risk genes, implicated cell types and drugs for repurposing based on known risk genes (derived from GWAS) for complex traits.
R Shiny application for the multi-omics analysis of inflammatory bowel disease
PhD thesis on data integration on inflammatory bowel disease
Reproducibility package for Mendelian randomization and dataset-matched colocalization across IBD and gut-joint-eye-skin immune comorbidity.
All QC, annotation, and analyses for IBD exomes
Quantitative metagenomic pipeline & Nextflow DSL2 workflow modeling intestinal protozoa–bacterial interactions in IBD dysbiosis using Compositional Data Analysis (CoDa) and leakage-free ML.
Reproducible pipeline for structuring and de-identifying abdominal radiology reports for clinical NLP research
Analysis code for the study Linkage analysis identifies novel genetic modifiers of microbiome traits in families with inflammatory bowel disease (Sharma et al., Gut Microbes, 2022).
Inflamed-vs-healed heatmaps for IBD colon biopsies: frozen pathology foundation-model (H-optimus-0) embeddings + attention-MIL, honestly validated leave-patients-out on public CC0 data. Research prototype, not clinical.
Reproducible topological data analysis and machine-learning study of inferred gut microbial metabolic networks in inflammatory bowel disease.
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