Page Index - iffatAGheyas/bioinformatics-tutorial-wiki GitHub Wiki
145 page(s) in this GitHub Wiki:
- Home
- Bioinformatics Tutorial Wiki
- 📘 Table of Contents
- 0. Prerequisites & Setup
- 1. Foundations
- 2. Sequence Analysis
- 3. Genomics & Variants
- 4. Transcriptomics
- 5. Proteomics & Structure
- 6. Advanced Topics
- 7. Reproducibility & Projects
- Adapter and Quality Trimming
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- Aligning Reads
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- Alignment Visualization
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- Amplicon Analysis
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- Annotation and Enrichment
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- BAM Processing with samtools
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- Basic VCF Operations
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- Biostatistics Refresher
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- Calling Variants
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- Coverage and Depth Analysis
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- Data Organization and Download
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- Data Types and Formats
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- Data Types‐Metagenomics
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- Differential Expression
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- Dimension Reduction and Clustering
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- Diversity and Statistical Analysis
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- DNA RNA Protein Basics
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- Experimental Design and Metadata
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- Filtering and Cleanup
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- Functional Enrichment
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- Functional Profiling
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- Genome Assembly Concepts
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- Hands On Exercise
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- Hands‐On Example
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- Hands‐On Exercise‐VC
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- Intro to Biopython and Bioconductor
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- MAG Quality and Annotation
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- Marker Detection and Differential Expression
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- Mass Spec Data Processing
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- Merging and Comparing VCFs
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- Metagenomic Assembly & Binning
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- Metagenomics
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- Multiple Sequence Alignment
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- Multi‐Omics and Batch Integration
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- Network and Systems Biology
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- Normalization and Exploratory Analysis
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- Normalization and Feature Selection
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- overview
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- Overview‐Metagenomics
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- Pairwise Alignment
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- Population Level Analyses
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- Post‐Alignment QC
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- Preprocessing and QC
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- Profile HMMs and Motif Finding
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- Protein Structure Visualization
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- Quality Filtering
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- Quantification and Count Matrix Generation
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- Raw Read Quality Control
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- Raw Read Quality Control‐Metagenomics
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- Read Alignment or Pseudo‐alignment
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- Read Mapping and SAM BAM
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- Reference Genome Preparation
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- RNA Seq Pipeline
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- SAM Format Deep Dive
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- Shotgun Taxonomic Profiling
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- Simulation and Benchmarking (Optional) ‐ Splatter (R) ‐ dyngen (Python)
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- Single Cell Omics
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- Structure Prediction AlphaFold
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- Trajectory and Pseudotime Analysis
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- Variant Calling
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- Variant Filtering Strategies
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- VC Overview
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- VCF Format Deep Dive
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- VCF Visualization
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- Visualization and Reporting
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- Visualization: Single Cell Omics
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- Workflow Management and Reproducibility
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