- Welcome to the Course!
- Course structure, aims and objectives
- Your first bioinformatic challenge!
- Quiz 1 file - an explanation
- What is this sequence?
- Quiz 1 walkthrough - undertaking a BLAST search
Online
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Quick facts
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Medium of instructions
English
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Mode of learning
Self study
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Mode of Delivery
Video and Text Based
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Course and certificate fees
Fees information
certificate availability
certificate providing authority
The syllabus
Introduction to the Course
Biology for differential gene expression analysis
- Biology for differential gene expression analysis - introduction
- What is this thing called bioinformatics?
- What is this thing called bioinformatics - quiz
- Overview of Gene Expression
- Translation of genetic code - theory
- Translation of genetic code - practice
- Open Reading Frame (ORF) translation
- Open Reading Frame translation walk-through
- Is genetic code redundant?
- Gene structure and splicing
- mRNA modifications
- Biology for differential gene expression analysis - section summary
Sequencing, PCR and Microarrays - Technical Foundation
- Lab techniques for differential gene expression analysis - intro
- Sequencing
- PCR
- Sanger sequencing
- Next generation sequencing
- Lab techniques for differential gene expression
- Microarrays
- Lab techniques for differential gene expression analysis - section summary
Experimental, Statistical and analytical foundation plus quantitative PCR
- First things first - RStudio installation
- Differential Gene Expression - fundamentals
- Sample preparation for differential gene expression analysis
- Measuring gene expression with qPCR
- qPCR quantification of gene expression
- qPCR quiz - part 1 - intro
- Is the expression of this tumour suppressor affected by this drug? - Part 1
- qPCR quiz walkthrough - part 1
- Experimental considerations for differential gene expression
- Statistical considerations for differential gene expression
- Spreadsheet qPCR analysis: preserving variability of expression
- Data analysis in RStudio
- Getting ready for your next quiz: dat package deprecation and functions
- Is the expression of this tumour suppressor affected by this drug? - Part 2 - Q1
- Is the expression of this tumour suppressor affected by this drug? - Part 2 - Q1
- Part 2 - Q1 Walkthrough
- Is the expression of this tumour suppressor affected by this drug? - Part 2 - Q2
- Is the expression of this tumour suppressor affected by this drug? - Part 2 - Q2
- Part 2 - Q2 walkthrough
- Is the expression of this tumour suppressor affected by this drug? - Part 2 - Q3
- Is the expression of this tumour suppressor affected by this drug? - Part 2 - Q3
- Part 2 - Q3 walkthrough
- Is the expression of this tumour suppressor affected by this drug? - Part 2 - Q4
- Is the expression of this tumour suppressor affected by this drug? - Part 2 - Q3
- Part 2 - Q4 walkthrough
A Deep dive into RNAseq and analysis methods
- Intro to RNAseq
- Analytical advantages of RNAseq and overview of RNAseq analysis pipeline
- RNAseq quick quizzes
- RNAseq analysis pipeline
- FastQC: assessing the quality of sequencing library
- Your FastQC exercise
- Should I trim this library of reads?
- FastQC exercise walkthrough
- Alignment (TUXEDO)
- alignment (Rsubread)
- Rsubread alignment quiz
- Rsubread alignment: stringent vs. less stringent alignment criteria
- Strict and less strict alignment quiz
- Strict and less strict alignment walkthrough
- Strict and less strict alignment quiz walkthrough
- Transcriptome assembly (TUXEDO)
- Installing Cuff-apps from TUXEDO toolkit
- Comparing genome annotations with Cuffcompare
- Cuffcompare genome annotation quiz
- Cuffcompare quiz walkthrough
- Read counts and FPKM/RPKM
- FPKM quiz
- Read counting (TUXEDO)
- Read counts (Rsubread)
- RPKM normalization (R)
- Convert read counts to RPKMs
- Convert read counts to RPKMs - quiz
- Quiz 18 - Code to get the answers walkthrough
- Differential gene expression (TUXEDO)
- General Linear Models (GLMs) for differential gene expression analysis - part 1
- GLMs for differential gene expression analysis - part 2
- GLMs for differential gene expression analysis - part 3
- GLMs for differential gene expression analysis - part 4
- GLMs quiz
- Design matrices for GLMs
- Further read count processing for differential expression analysis
- Differential expression (R's GLM): limma, edgeR
- Differential expression: impact of filtering & normalization
- Differential expression quiz
- Differential expression quiz walkthrough
- Differential expression: RankProd
- Differential expression with RankProd in R
- RankProd Quiz
- RankProd Quiz walkthrough
Pathway analysis for hypothesis generation
- Hands on ORA-based pathway analysis
- ORA Quiz
- Hands on GSEA-based pathway analysis
- GSEA Quiz
- Using pathway analysis in hypothesis-free studies
Gene Expression Analysis
- Visualization of gene expression data
- Using Venny for venn diagram analysis
- Using Venny for venn diagram analysis - quiz
- Learn to visualize gene expression data in R
- Visualization of gene expression data hands on exercise
Your Capstone project
- Capstone project
- Capstone project materials
Instructors
Mr Alexander Abdulkader Kheirallah
instructor
Freelancer
Other Bachelors, Ph.D