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🧬
Research
🧬
Research

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nkirtipal/README.md

🔬 Current Research

Taking human disease apart across layers — single cells, microbes, and molecules.

Current areas

  • 🫁 Respiratory disease and COPD
  • 🫧 Single-cell transcriptomics
  • 🧪 Multi-omics integration
  • 🤖 Interpretable machine learning for biological discovery
  • 🧫 Disease and cancer genomics

💻 Computational Toolkit

Area Methods & Tools
Programming R · Python · Bash
Single-cell Seurat · Scanpy · SingleR · CellChat · SCENIC · Monocle
Bulk RNA-seq DESeq2 · WGCNA
Microbiome DADA2 · phyloseq · MMUPHin · MaAsLin2
Metagenomics MetaPhlAn · HUMAnN — bioBakery
Machine Learning Random Forest · XGBoost · SHAP
Deep Learning PyTorch · CNN
Dimensionality Reduction PCA · PCoA · UMAP
Statistics PERMANOVA · differential abundance · survival analysis
Workflow / HPC Snakemake · SLURM
Cancer Genomics TCGA · GTEx · Xena · MAF
Visualization ggplot2 · ComplexHeatmap · Cytoscape

🧪 Computational Biology Workflow

Biological Question
          │
          ▼
   Data Generation
          │
          ▼
 ┌─────────────────────┐
 │ Multi-Omics Data    │
 │                     │
 │ RNA-seq             │
 │ scRNA-seq           │
 │ Microbiome          │
 │ Metagenomics        │
 └─────────────────────┘
          │
          ▼
 Data Processing & QC
          │
          ▼
 Statistical Analysis
          │
          ▼
 ┌─────────────────────┐
 │ Computational       │
 │ Modeling            │
 │                     │
 │ ML · Network        │
 │ Regulatory Biology  │
 └─────────────────────┘
          │
          ▼
 Biological Interpretation
          │
          ▼
      Insight



🧬 Background


Wet-lab 🧪 biologist turned computational researcher — driven by biological questions, building tools and pipelines whenever the biology demands it.






🧬 Always learning — from 🧪 pipettes to 🐍 pipelines!

Pinned Loading

  1. NikSeqRecur NikSeqRecur Public

    Recurrence-aware DNA sequence analysis tool for repeat detection, mutation annotation, and genomic visualization.

    Python

  2. Bioimage_ML_Classification Bioimage_ML_Classification Public

    CNN-based bioimage classification for biological phenotype detection using machine learning and Explainable AI

    Jupyter Notebook

  3. Diabetes-ML-DL-Comparison Diabetes-ML-DL-Comparison Public

    Seven models, one evaluation protocol, bootstrap confidence intervals, and interpretability analysis - comparing classical machine learning and deep learning for diabetes prediction.

    Jupyter Notebook

  4. Celltype-Annotation-Benchmark Celltype-Annotation-Benchmark Public

    Reproducible benchmark of four scRNA-seq cell type annotation methods (SingleR, CellTypist, ACTINN, scANVI) on PBMC3K

    Jupyter Notebook

  5. Survival-Analysis-R Survival-Analysis-R Public

    R workflow for survival analysis: Kaplan-Meier, Cox regression, and summary tables

    R

  6. maftools-TCGA-LUAD maftools-TCGA-LUAD Public

    Somatic mutations in TCGA lung adenocarcinoma — maftools workflow

    R