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Bioinformatics Methods for Transcriptomics

Bioinformatics Methods for Transcriptomics

位教师：Liliana Florea, PhD

4,893 人已注册

包含在中

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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

您将学习的工具

要了解的详细信息

可分享的证书

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作业

8 项作业

授课语言：英语（English）

91% of learners achieved a positive career outcome

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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.

单元详情

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 Introduction6分钟
Gene expression analysis of RNA-seq data3分钟
Step 1: Downloading and Preparing the Data9分钟
Step 2: Aligning the RNA-seq reads11分钟
Step 3: Assembling the Genes and Transcripts, Part 111分钟
Step 3: Assembling the Genes and Transcripts, Part 211分钟
Step 4: Determining the Differentially Expressed Genes, Part 13分钟
Step 4: Determining the Differentially Expressed Genes, Part 211分钟
Step 4: Determining the Differentially Expressed Genes, Part 36分钟
Step 4: Determining the Differentially Expressed Genes, Part 410分钟
Step 4: Determining the Differentially Expressed Genes, Part 513分钟
Step 5: Visualizing the Data, Part 14分钟
Step 5: Visualizing the Data, Part 29分钟

5篇阅读材料总计45分钟

Course Syllabus10分钟
Virtual Environment Setup10分钟
Coursera Manual and Technical Support 10分钟
List of software packages10分钟
Forums for Module or Technical Questions5分钟

2个作业总计140分钟

Checks for Understanding: Module 120分钟
Module 1 Graded Project120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 19分钟
Introduction to alternative splicing (AS) analysis, Part 24分钟
Introduction to alternative splicing (AS) analysis, Part 32分钟
Step 1: Preparing the input data 2分钟
Step 2: Isoform-level analysis with Cuffdiff211分钟
Step 3: Event-level analysis with rMATS, Part 110分钟
Step 3: Event-level analysis with rMATS, Part 23分钟
Step 3: Event-level analysis with rMATS, Part 38分钟
Step 4A: Intron-level analysis with MntJULiP, Part 1 10分钟
Step 4A: Intron-level analysis with MntJULiP, Part 28分钟
Step 4A: Intron-level analysis with MntJULiP, Part 35分钟
Step 4A: Intron-level analysis with MntJULiP, Part 47分钟
Step 4B: Intron-level analysis with MntJULiP II8分钟
Step 5A: Intron retention analysis with IRFinder, Part 15分钟
Step 5A: Intron retention analysis with IRFinder, Part 22分钟
Step 5A: Intron retention analysis with IRFinder, Part 39分钟
Step 5B: Intron retention analysis with IRFinder II, Part 18分钟
Step 5B: Intron retention analysis with IRFinder II, Part 25分钟
Step 6A: AS visualization with IGV and Jutils I, Part 15分钟
Step 6A: AS visualization with IGV and Jutils I, Part 27分钟
Step 6B: AS visualization with Jutils II, Part 19分钟
Step 6B: AS visualization with Jutils II, Part 2 5分钟
Step 6B: AS visualization with Jutils II, Part 37分钟
Step 6B: AS visualization with Jutils II, Part 46分钟

2个作业总计140分钟

Checks for Understanding: Module 220分钟
Module 2 Graded Project120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 reads6分钟
Preparing the input sequence data5分钟
Aligning the long RNA sequencing reads, Part 19分钟
Aligning the long RNA sequencing reads, Part 26分钟
Building transcript models with FLAIR (align)10分钟
Building transcript models with FLAIR8分钟
Building transcript models with FLAIR (collapse), Part 17分钟
Building transcript models with FLAIR (collapse), Part 211分钟
Building transcript models with FLAIR (quantify) 6分钟
Building transcript models with IsoQuant, Part 110分钟
Building transcript models with IsoQuant, Part 25分钟
Building transcript models with IsoQuant, Part 39分钟
Visualizing transcript data with the IGV, Part 14分钟
Visualizing transcript data with the IGV, Part 210分钟

2个作业总计140分钟

Checks for Understanding: Module 320分钟
Module 3 Graded Project120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 sequencing8分钟
Preparing the data - a review4分钟
Differential gene and transcript expression (DESeq2), Part 112分钟
Differential gene and transcript expression (DESeq2), Part 29分钟
Differential splicing detection with short read tools (FLAIR drimSeq and DESeq2), Part 111分钟
Differential splicing detection with short read tools (FLAIR drimSeq and DESeq2), Part 29分钟
Differential splicing detection with short read tools (FLAIR diffSplice), Part 14分钟
Differential splicing detection with short read tools (FLAIR diffSplice), Part 28分钟
Differential splicing detection with short read tools (FLAIR diffSplice), Part 34分钟
Differential splicing detection with long read tools (1) (LIQA), Part 17分钟
Differential splicing detection with long read tools (1) (LIQA), Part 211分钟
Differential splicing detection with long read tools (2) (LIQA), Part 15分钟
Differential splicing detection with long read tools (2) (LIQA), Part 29分钟
Differential splicing detection with long read tools (2) (LIQA), Part 36分钟
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