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    Pathway Enrichment With Gprofiler, Clusterprofiler And Fgsea

    Posted By: ELK1nG
    Pathway Enrichment With Gprofiler, Clusterprofiler And Fgsea

    Pathway Enrichment With Gprofiler, Clusterprofiler And Fgsea
    Published 2/2024
    MP4 | Video: h264, 1920x1080 | Audio: AAC, 44.1 KHz
    Language: English | Size: 1.14 GB | Duration: 2h 23m

    Learn how to perform OverRepresentation Analysis (ORA) and Functional Class Scoring (FCS) analysis.

    What you'll learn

    How overrepresentation analysis works

    How functional class scoring works

    How to perform pathway enrichment analysis

    How to visualize the results

    Requirements

    Basic R programming skills

    Description

    Hello everyone!This course focuses on exploring the biological pathways associated with a list of genes. More specifically, it focuses on knowledge-based pathway enrichment analysis through methods such as OverRepresentation Analysis (ORA) and Functional Class Scoring (FCS). At the end of this course you should be able to perform ORA using two of the most commonly used tools, gProfiler and clusterProfiler. You should also be able to perform FCS analysis by using clusterProfiler and fgsea packages. You will also learn how to choose the top results,  how to visualize these results using two different kinds of plots and also how to plot the expression of the core genes associated with a specific pathway that might hold biological significance in your data.If you are eager to extract biological insight from a list of genes of interest you have on your hands, or if you plan on diving in the world of transcriptomics data analysis, the analyses mentioned in this course are a must.So, get in your learning mood and start the course to learn one of the most commonly used bioinformatics analyses!P.S. You also get to keep the script for use with your own gene lists and datasets! Neat!

    Overview

    Section 1: Introduction

    Lecture 1 File Structure

    Lecture 2 Introduction

    Lecture 3 Basic R commands and data structures

    Lecture 4 Installing the required libraries

    Lecture 5 Basic Dplyr Info

    Section 2: Pathway Enrichment

    Lecture 6 Brief explanation of pathway enrichment methods

    Lecture 7 Description of available data

    Lecture 8 Setting up Overrepresentation analysis (ORA)

    Lecture 9 Gathering Gene sets

    Lecture 10 ORA using gProfiler

    Lecture 11 ORA using clusterProfiler

    Lecture 12 Comparing ORA results

    Lecture 13 Preparing ranked gene list and FCS using clusterProfiler

    Lecture 14 FCS using fgsea

    Lecture 15 Comparing FCS results

    Section 3: Visualizing results

    Lecture 16 Creating an enrichment bubble plot for gProfiler

    Lecture 17 Creating an enrichment bubble plot for clusterProfiler's ORA

    Lecture 18 Creating an enrichment bubble plot for clusterProfiler's FCS

    Lecture 19 Plotting fgsea results

    Lecture 20 Plotting a leading egde gene expression heatmap

    Section 4: Reproducibility

    Lecture 21 Reproducibility and closing remarks

    Intermediate or Advanced R users aiming to delve more into bioinformatics