0. Introduction to the course "Applied Bioinformatics 2023" - 22/07/2023
Please select a project before 09/09/2023
1. Linux Operating System (OS), Linux command lines, basic bash script, and awk - 22/07/2023
1.1 Linux OS Ubuntu and Linux command lines
1.2 Basic bash script and awk and Practice on bash script
2. Basic Introduction to R, Data Visualization, and Statistics with R - 29/07/2023
2.1 Introduction to Basic R1 and R2
2.2 Data Visualization with R3 and R4
2.3 Some Basic Statistics with R5 and R6
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Quiz
3. Review basic molecular biology, the human genome, gene annotation, and the other databases - 05/08/2023
3.1 Nucleotide DNA & RNA
3.2 Human Genome Structure, Function, and Clinical Considerations
4. Basic GWAS with case vs control and quantitative traits - 12/08/2023
4.1 Introduction to GWAS
5. Next-Generation Sequencing and upstream analysis for DNA-seq - 19/08/2023
5.1 Introduction to NGS platform
5.2 Raw Data Processing and Alignment/Mapping for DNA-seq
6. Downstream analysis for DNA-seq - 26/08/2023
6.1 Variant Calling and Variant Filtering for DNA-seq
6.2a Variant Annotation and Variant Annotation databases for DNA-seq Part I
6.2b Variant Annotation and Variant Annotation databases for DNA-seq Part II
6.3 Cancer Gene Panel DNA testing
Practice on DNA-seq Downstream Analysis
7. Introduction to bulk RNA-seq, library types, and experiment design - 9/09/2023
7.1 Introduction to transcriptome, bulk RNA-seq and microarray
7.2 Comparison of Expression Array vs RNA-seq
7.3 RNA-seq library types and Bulk RNA-seq experimental design
8. PolyA bulk RNA-seq analysis - 16/09/2023
8.1 Upstream analysis with mapping to reference genome and De novo assembly
8.2a Downstream analysis of bulk RNA-seq Part I
8.2b Downstream analysis of bulk RNA-seq Part II
8.3 Use cases of poly-A bulk RNA-seq for variant calling
9. Long non-coding bulk RNA-seq analysis - 23/09/2023
9.1 Use cases of long non-coding RNA and allelic gene expression
10. Presenting group projects
List of group projects for Applied Bioinformatics