RNAseq Data analysis using Shell scripting and R
RNAseq Data analysis using Shell scripting and R, available at $19.99, has an average rating of 3.89, with 20 lectures, based on 9 reviews, and has 50 subscribers.
You will learn about Basics of NGS data analysis and how to perform Differential gene expression analysis for RNAseq dataset Generating Quality Control metrics and statistics Mapping Reads to the genome Differential gene expression Using Conda for installation of bioinformatics tools Processing RNA sequencing data UNIX command-line tools for processing the data Transcript quantification Performing Principal Component Analysis (PCA) Performing Clustering analysis using gene expression data This course is ideal for individuals who are People interested in learning Next Generation Sequencing data analysis methods or Beginner Bioinformatician looking to understand end-to-end pipeline for transcriptomics data analysis or People looking to understand differential gene expression analysis or People interested to carry out bioinformatics analysis with command-line tools It is particularly useful for People interested in learning Next Generation Sequencing data analysis methods or Beginner Bioinformatician looking to understand end-to-end pipeline for transcriptomics data analysis or People looking to understand differential gene expression analysis or People interested to carry out bioinformatics analysis with command-line tools.
Enroll now: RNAseq Data analysis using Shell scripting and R
Summary
Title: RNAseq Data analysis using Shell scripting and R
Price: $19.99
Average Rating: 3.89
Number of Lectures: 20
Number of Published Lectures: 20
Number of Curriculum Items: 20
Number of Published Curriculum Objects: 20
Original Price: £34.99
Quality Status: approved
Status: Live
What You Will Learn
- Basics of NGS data analysis and how to perform Differential gene expression analysis for RNAseq dataset
- Generating Quality Control metrics and statistics
- Mapping Reads to the genome
- Differential gene expression
- Using Conda for installation of bioinformatics tools
- Processing RNA sequencing data
- UNIX command-line tools for processing the data
- Transcript quantification
- Performing Principal Component Analysis (PCA)
- Performing Clustering analysis using gene expression data
Who Should Attend
- People interested in learning Next Generation Sequencing data analysis methods
- Beginner Bioinformatician looking to understand end-to-end pipeline for transcriptomics data analysis
- People looking to understand differential gene expression analysis
- People interested to carry out bioinformatics analysis with command-line tools
Target Audiences
- People interested in learning Next Generation Sequencing data analysis methods
- Beginner Bioinformatician looking to understand end-to-end pipeline for transcriptomics data analysis
- People looking to understand differential gene expression analysis
- People interested to carry out bioinformatics analysis with command-line tools
In this course, you will learn how to perform RNAseq data analysis via linux command line. This course provides a comprehensive introduction to RNAseq data analysis, covering the key concepts and tools needed to perform differential expression analysis and functional annotation of RNAseq data. Students will learn how to preprocess raw sequencing data, perform quality control, and align reads to a reference genome or transcriptome. The course will also cover differential expression analysis using statistical methods and visualisation of results using popular tools such as R. You will learn how to do end-to-end RNAseq data analysis which includes pre-processing of RNAseq data, Quality Control analysis, Differential Gene Expression analysis, Clustering and Principal Component Analysis of the gene expression data. You will also learn how to download data, install the bioinformatics/IT softwares using Conda/Anaconda on Mac, Windows or Linux platforms. I will guide you through performing differential expression analysis on RStudio (graphical user interface for R language).
Throughout the course, students will work with real-world datasets and gain hands-on experience with popular bioinformatics tools and software packages. By the end of the course, students will have a thorough understanding of RNAseq data analysis and will be able to perform their own analyses of gene expression data. This course is ideal for researchers, scientists, and students who are interested in understanding the molecular basis of gene expression and exploring the potential applications of RNAseq technology. No prior bioinformatics or programming experience is required, but a basic knowledge of molecular biology and genetics is recommended.
Course Curriculum
Chapter 1: Introduction and Installation
Lecture 1: Introduction
Lecture 2: Installing Conda
Lecture 3: Installing Bioinformatics tools using Conda
Chapter 2: Preparing Data for Analysis
Lecture 1: Organising the files
Lecture 2: Obtaining the Raw Data
Lecture 3: Obtaining the Genome files
Chapter 3: Quality Control of RNA-seq data
Lecture 1: QC analysis using FastQC for Single-End and Paired-End reads
Chapter 4: Read Trimming and QC analysis
Lecture 1: Adaptor and Quality Trimming using Trimmomatic
Lecture 2: QC analysis of Trimmed Reads using MultiQC
Chapter 5: Genome Indexing and Read Mapping
Lecture 1: Genome Indexing using STAR
Lecture 2: Read Mapping using STAR
Chapter 6: Duplicate Read Marking
Lecture 1: Marking Duplicate reads using Picard and indexing BAM files
Chapter 7: Obtaining Alignment Statistics
Lecture 1: Printing Alignment statistics using Bamtools
Chapter 8: Obtaining Counts (read abundance) using FeatureCounts
Lecture 1: Generating Gene Counts for DE analysis
Chapter 9: Differential Expression (DE) analysis using DESeq2 on RStudio
Lecture 1: Preparing the files for DE analysis
Lecture 2: Installing libraries for DE analysis on RStudio
Lecture 3: Performing the DE analysis using DESeq2 – Part1
Lecture 4: Performing the DE analysis using DESeq2 – Part2
Chapter 10: Principal Component Analysis and Clustering analysis of gene expression data
Lecture 1: Performing PCA analysis and generating PCA plot
Lecture 2: Performing Clustering analysis of gene expression data
Instructors
-
Sumukh Deshpande
Bioinformatician
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- 3 stars: 4 votes
- 4 stars: 3 votes
- 5 stars: 2 votes
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