Genomics, Bioinformatics and Molecular Data Science

Module 1: Foundations of NGS Data, Quality Control, and Read Preprocessing

Module 2: High-Accuracy Read Alignment and Post-Alignment Processing

Module 3: Small Variant Calling Frameworks (SNVs and Indels)

Module 4: Somatic Variant Calling and Cancer Genomics

Module 5: Structural Variation (SV) Detection in Short-Read Data

Module 6: Long-Read Genomics for Structural Variant Discovery

Module 7: Copy Number Variation (CNV) Analysis and Detection

Module 8: Variant Annotation, Filtering, and Functional Effect Prediction

Module 9: Automated Workflow Management with Nextflow and Snakemake

Module 10: Containerization, HPC Deployment, and Pipeline Reproducibility

Module 1: Single-Cell Technologies, Experimental Design, and Raw Data Processing

Module 2: Quality Control, Filtering, and Doublet Identification

Module 3: Data Normalization, Variance Stabilization, and Feature Selection

Module 4: Dimensionality Reduction, Batch Effect Correction, and Data Integration

Module 5: Unsupervised Cell Clustering and Subpopulation Identification

Module 6: Differential Gene Expression Analysis and Marker Gene Identification

Module 7: Automated Cell Type Annotation and Reference Mapping

Module 8: Trajectory Inference, Pseudotime Modeling, and RNA Velocity

Module 9: Cell-Cell Communication Analysis and Ligand-Receptor Interaction Modeling

Module 10: Multi-Modal Single-Cell Omics and Spatial Transcriptomics Integration

Module 1: Introduction to Transcriptomics, Experimental Design, and Next-Generation Sequencing

Module 2: Linux Command Line and High-Performance Computing for Genomics

Module 3: Raw Data Quality Control, Preprocessing, and Read Trimming

Module 4: Reference-Based Read Alignment and Pseudo-Alignment Strategies

Module 5: Gene and Transcript Quantification

Module 6: Differential Gene Expression (DGE) Analysis in R

Module 7: Functional Enrichment, Pathway Mapping, and Systems Biology

Module 8: Single-Cell RNA Sequencing (scRNA-Seq) Data Processing

Module 9: Long-Read Transcriptomics, Isoform Analysis, and Alternative Splicing

Module 10: Reproducible Research, Pipeline Automation, and Multi-Omics Integration