Bioinformatics Methods for Transcriptomics

Bioinformatics Methods for Transcriptomics

位教师：Liliana Florea, PhD

访问权限由 Coursera Learning Team 提供

4,375 人已注册

4个模块

深入了解一个主题并学习基础知识。

中级等级

需要一些相关经验

2 周完成

在 10 小时一周

灵活的计划

自行安排学习进度

4个模块

深入了解一个主题并学习基础知识。

中级等级

需要一些相关经验

2 周完成

在 10 小时一周

灵活的计划

自行安排学习进度

您将获得的技能

要了解的详细信息

可分享的证书

添加到您的领英档案

作业

8 项作业

授课语言：英语（English）

了解顶级公司的员工如何掌握热门技能

了解关于 Coursera for Business 的更多信息

Petrobras, TATA, Danone, Capgemini, P&G 和 L'Oreal 的徽标

该课程共有4个模块

This course will cover bioinformatics methods for analyzing transcriptomic RNA sequencing data generated with the short read (RNA-seq) and long read (PacBio, ONT) sequencing. In its four modules, the course addresses the core transcriptomics questions: What are the genes and transcripts expressed in a given sample or condition of an experiment?, What are their expression levels?, and What are the differences in gene expression and splicing patterns between conditions? It provides hands-on instruction on how to use popular and/or emerging tools such as STAR, PsiCLASS, DESeq2, rMATS, MntJULiP, Minimap2 and IsoQuant. This is an intermediate level course, and assumes basic knowledge on using command line bioinformatics tools in a Unix-type environment.

涵盖的内容

13个视频5篇阅读材料2个作业

13个视频总计106分钟

Course Introduction 6分钟
Gene expression analysis of RNA-seq data 3分钟
Step 1: Downloading and Preparing the Data 9分钟
Step 2: Aligning the RNA-seq reads 11分钟
Step 3: Assembling the Genes and Transcripts, Part 1 11分钟
Step 3: Assembling the Genes and Transcripts, Part 2 11分钟
Step 4: Determining the Differentially Expressed Genes, Part 1 3分钟
Step 4: Determining the Differentially Expressed Genes, Part 2 11分钟
Step 4: Determining the Differentially Expressed Genes, Part 3 6分钟
Step 4: Determining the Differentially Expressed Genes, Part 4 10分钟
Step 4: Determining the Differentially Expressed Genes, Part 5 13分钟
Step 5: Visualizing the Data, Part 1 4分钟
Step 5: Visualizing the Data, Part 2 9分钟

5篇阅读材料总计45分钟

Course Syllabus 10分钟
Virtual Environment Setup 10分钟
Coursera Manual and Technical Support 10分钟
List of software packages 10分钟
Forums for Module or Technical Questions 5分钟

2个作业总计140分钟

Module 1 Graded Project 120分钟
Checks for Understanding: Module 1 20分钟

涵盖的内容

24个视频2个作业

24个视频总计155分钟

Introduction to alternative splicing (AS) analysis, Part 1 9分钟
Introduction to alternative splicing (AS) analysis, Part 2 4分钟
Introduction to alternative splicing (AS) analysis, Part 3 2分钟
Step 1: Preparing the input data 2分钟
Step 2: Isoform-level analysis with Cuffdiff2 11分钟
Step 3: Event-level analysis with rMATS, Part 1 10分钟
Step 3: Event-level analysis with rMATS, Part 2 3分钟
Step 3: Event-level analysis with rMATS, Part 3 8分钟
Step 4A: Intron-level analysis with MntJULiP, Part 1 10分钟
Step 4A: Intron-level analysis with MntJULiP, Part 2 8分钟
Step 4A: Intron-level analysis with MntJULiP, Part 3 5分钟
Step 4A: Intron-level analysis with MntJULiP, Part 4 7分钟
Step 4B: Intron-level analysis with MntJULiP II 8分钟
Step 5A: Intron retention analysis with IRFinder, Part 1 5分钟
Step 5A: Intron retention analysis with IRFinder, Part 2 2分钟
Step 5A: Intron retention analysis with IRFinder, Part 3 9分钟
Step 5B: Intron retention analysis with IRFinder II, Part 1 8分钟
Step 5B: Intron retention analysis with IRFinder II, Part 2 5分钟
Step 6A: AS visualization with IGV and Jutils I, Part 1 5分钟
Step 6A: AS visualization with IGV and Jutils I, Part 2 7分钟
Step 6B: AS visualization with Jutils II, Part 1 9分钟
Step 6B: AS visualization with Jutils II, Part 2 5分钟
Step 6B: AS visualization with Jutils II, Part 3 7分钟
Step 6B: AS visualization with Jutils II, Part 4 6分钟

2个作业总计140分钟

Module 2 Graded Project 120分钟
Checks for Understanding: Module 2 20分钟

涵盖的内容

14个视频2个作业

14个视频总计105分钟

Introduction to transcriptomics with long RNA sequencing reads 6分钟
Preparing the input sequence data 5分钟
Aligning the long RNA sequencing reads, Part 1 9分钟
Aligning the long RNA sequencing reads, Part 2 6分钟
Building transcript models with FLAIR (align) 10分钟
Building transcript models with FLAIR 8分钟
Building transcript models with FLAIR (collapse), Part 1 7分钟
Building transcript models with FLAIR (collapse), Part 2 11分钟
Building transcript models with FLAIR (quantify) 6分钟
Building transcript models with IsoQuant, Part 1 10分钟
Building transcript models with IsoQuant, Part 2 5分钟
Building transcript models with IsoQuant, Part 3 9分钟
Visualizing transcript data with the IGV, Part 1 4分钟
Visualizing transcript data with the IGV, Part 2 10分钟

2个作业总计140分钟

Module 3 Graded Project 120分钟
Checks for Understanding: Module 3 20分钟

涵盖的内容

15个视频2个作业

15个视频总计108分钟

Introduction to differential expression and splicing analysis with long read RNA sequencing 8分钟
Preparing the data - a review 4分钟
Differential gene and transcript expression (DESeq2), Part 1 12分钟
Differential gene and transcript expression (DESeq2), Part 2 9分钟
Differential splicing detection with short read tools (FLAIR drimSeq and DESeq2), Part 1 11分钟
Differential splicing detection with short read tools (FLAIR drimSeq and DESeq2), Part 2 9分钟
Differential splicing detection with short read tools (FLAIR diffSplice), Part 1 4分钟
Differential splicing detection with short read tools (FLAIR diffSplice), Part 2 8分钟
Differential splicing detection with short read tools (FLAIR diffSplice), Part 3 4分钟
Differential splicing detection with long read tools (1) (LIQA), Part 1 7分钟
Differential splicing detection with long read tools (1) (LIQA), Part 2 11分钟
Differential splicing detection with long read tools (2) (LIQA), Part 1 5分钟
Differential splicing detection with long read tools (2) (LIQA), Part 2 9分钟
Differential splicing detection with long read tools (2) (LIQA), Part 3 6分钟
Closing 0分钟