DESeq2 workflow tutorial | Differential Gene Expression Analysis | Bioinformatics 101

Опубликовано: 22 Январь 2022
на канале: Bioinformagician

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A walk-through of steps to perform differential gene expression analysis in a dataset with human airway smooth muscle cell lines to understand transcriptome changes in response to asthma medications.

DESeq2 Vignette:
http://bioconductor.org/packages/rele...

Link to Code:
Code to get data: https://github.com/kpatel427/YouTubeT...
DESeq2 workflow: https://github.com/kpatel427/YouTubeT...

Additional resources:
1. https://bioc.ism.ac.jp/packages/2.14/...
2. https://bioconductor.org/packages/rel...
3. https://lashlock.github.io/compbio/R_...
4. https://genviz.org/module-04-expressi...

Chapters
0:00 Intro
0:45 Study design
2:30 Preparing counts data
5:41 Create DESeqDataSet (dds) object
9:51 Setting reference level
11:20 Run DESeq()
12:35 results after running DESeq()
14:14 Multiple testing correction (adjust p-values)
15:06 Exploring results
16:07 Contrasts
17:53 MA plot (Visualize DE genes)

Show your support and encouragement by buying me a coffee:
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To get in touch:
Website: https://bioinformagician.org/
Github: https://github.com/kpatel427
Email: [email protected]

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