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    Differential Gene Expression Analysis - Your Complete A to Z

    BY
    Udemy

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    Mode

    Online

    Fees

    ₹ 3299

    Quick Facts

    particular details
    Medium of instructions English
    Mode of learning Self study
    Mode of Delivery Video and Text Based

    Course and certificate fees

    Fees information
    ₹ 3,299
    certificate availability

    Yes

    certificate providing authority

    Udemy

    The syllabus

    Introduction to the Course

    • 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

    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

    Mr Alexander Abdulkader Kheirallah
    instructor
    Freelancer

    Other Bachelors, Ph.D

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