Comprehensive Bioinformatics: Learn Genomics Data Analysis

سرفصل های دوره

Unlocking Genomic Data Analysis Mysteries through Practical Bioinformatics Applications for Research Purpose

1. Introduction

1. Introduction to Genomics for Bioinformatics

2. Sequence Alignment

1. Pairwise Sequence Alignment

2. Multiple Sequence Alignment

3. Sequence Alignment Using Mega

3. Genome Annotation Analysis

1. Genome Annotation and visualization

4. Gene Structure Analysis

1. Intron and Exon Analysis

5. Linux in Bioinformatics (optional)

1. Introduction and Why CLI in Bioinformatics

2. CLI and GUI Explanation

3. if we already have Graphical user interface system why we should use CLI

4. Short Practical with Programming Language

5. Why Would You Use CLI over GUI

6. Drawbacks of CLI and GUI

7. Foundation behind CLI Shell explanation

8. Linux Introduction and Usage Over years

9. Linux Distros

10. Why Ubuntu Operating System

11. WSL Explanation

12. Linux Vs Unix

13. (Practical) Making A Subsystem For Linux In Windows OS

14. Linux File Handling Commands

15. Accessing And Creating Files In Windows Os

16. Basic Process Management Commands for Linux OS

17. E-utilities on the Linux Command Line

18. Installing NCBI through CLi

19. Entrez Direct Functions

20. Mrna And Protein Seq Retrieval

21. Batch Retrieval of Protein Using Taxon Id

22. Retrieving CDS From Reference Genome

23. Explaining Different Commands

24. Commands.html

6. Variant Calling Analysis on Linux

1. Introduction of Course Section

2. Variants and Types

3. Understanding the Metadata and Softwares

4. Getting Data From SRA Using SRA Toolkit

5. Quality Control and Trimming

6. Sam and Bcf Tools and Fixing NS and Calling Variants

7. Alignment to Reference Genome

8. Separation of SNPs and Indels Variants

9. Visualizing Variants Using IGV and UCSC Browser

10. Pipeline Code.html

7. Gene location on Chromosome

1. Gene location on Chromosome Analysis

8. Transcriptomics (NGS Data) Analysis using GUI and CLI

1. Introduction of Course Section

2. Next-generation sequencing

3. Generations of Sequencing

4. NGS Workflow

5. SRA Database introduction

6. SRA File

7. Galaxy Server Intro to Goals

8. Galaxy Server And Objects

9. Getting Onto Galaxy

10. Tools For NGS Data Analysis

11. Getting SRA Runs from Databases And platform

12. Ncbi Genome to Galaxy

13. Getting Sra Runs To Galaxy

14. Fastqc Tool To Dataset Generated Dataset

15. Trimmomatic Tool On Dataset

16. Alignmentgenome Mapping

17. Abundance Estimation Tool On Dataset

18. From Values To Visuals (Heatmap)

19. Understanding NGS For Linux

20. Getting the SRA Reads

21. Bioinformatics Pipeline

22. Checking the Quality of Data

23. Quality Trimming of data

24. Aligners and Aligning Reads to genome

25. SAM and Bam File Indexing and Sorting

26. Feature Extraction

27. Pipeline Code.html

9. Proteomics

1. Protein Structure Prediction

2. Homology Modeling

3. GUI based Modeling of Proteins

4. Command Line based Protein Modeling

5. De-Novo and Machine Learning Modeling

6. Protein Visualization Analysis

7. Motifs and Domains analysis

8. Protein Physical Parameters and Location Analysis

9. Protein Pathway and Enrichment Analysis

10. Protein-Protein Interaction Network

11. Proteins Pathway Analysis

10. Phylogenetics

1. Phylogenetics Analysis

11. Functional Genomics

1. Gene Enrichment Analysis

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تولید کننده: Udemy