oguzhanpanatli / miuul

Miuul Bioinformatics Bootcamp-2024

This repository contains materials related to Miuul Bioinformatics Bootcamp.

Contents

1. What is Bioinformatics?

   • Introduction to the fundamentals and application areas of bioinformatics.

2. Setups: PyCharm, GitHub, Anaconda

   • Installation guides for tools necessary for bioinformatics projects.

3. Introduction to Python & Linux

   • Basic information on the Python programming language and the Linux operating system.

4. Workflow management with Snakemake

   • tRNA scanning rules with Snakemake.

5. Databases: NCBI Genome, IPR Domains

   • Overview of important databases used in bioinformatics research.

6. tRNA Scanning

   • Usage of tRNA wild card and visualization with scatter plots.

7. NGS & Genome Assembly and Annotation

   • Introduction to PacBio, Illumina, Nanopore technologies, and contig, gff, fasta formats.

8. Advanced BLAST

   • BLAST parameters and graphical visualization of results.

9. Functional Annotation

   • Analysis with Interproscan, IPR, superfamilies, and domains.

10. Functional Annotation with Heatmap Plot

    • Visualization of results with a heatmap.

11. Comparative Genomics: Orthologs, Paralogs, Orthofinder

    • 1:1 and 1:M orthology analyses.

12. Comparative Genomics: Heatmap, Upset Plot

    • Visualization techniques used for comparative analysis of genomic data.

13. Metabolic Analysis: Ipath

    • Analysis and visualization of metabolic pathways.

14. Transposable Elements (TE)

    • Analysis of TEs with RepeatMasker and stained glass technique.

License

© 2024 Zeynep Akdeniz

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