How I analyze RNA Seq Gene Expression data using DESeq2

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Chapters

00:00 Intro
02:43 Load R libraries
03:38 Load the dataset
07:11 Set the factors
08:19 Create deseq DESeqDataSetFromMatrix() dds object and import coutn data and sample information
11:37 Filter genes
14:08 Perform statistical tests to identify differentially expressed genes (result dds)
18:34 Order the deseq_result
20:48 Make queries
24:20 Filter differentially expressed genes.
28:45 Save deseq result
31:28 Examine the output files
33:06 Visualize deseq result
33:24 Plot dispersions
35:30 PCA Plot
43:08 Heatmaps
44:11 Heatmap of sample-sample distance matrix using pheatmap
52:37 Heatmap of log transformed normalized counts using pheatmap
1:02:18 Heatmap Z-scores
1:06:51 MA Plot
01:11:37 Volcano plot using ggplot
01:16:31 Next Tutorial

DESeq2 R Tutorial

Transcriptomics
RNA-Seq Analysis
RNASeq
RNA Seq
Gene expression
RNA Seq Analysis - Bioinformatics Project
DESeq2 tutorial for gene expression analysis

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[charithr]

Hi Bioinformatics Coach,
Your dedication to helping your viewers is evident, and it sets you apart from others. It's incredibly valuable to have someone like you who genuinely cares about the community and goes above and beyond to provide assistance. Your quick replies make a real impact, and I wanted to make sure you know how much it means to me.

[feelingless-is-meaningless]

Excellent work, Great effort, Great dedication.

[반규리-so]

First of all, thank you for this tutorial:)
When you load the count data, what if the data is a "bam" format instead of "csv" format??

[darshakmangukiya]

i have problem in dds <-DGEs matrix .... code how to solve this error
Error in DESeqDataSet(se, design = design, ignoreRank) :
some values in assay are not integers. can you help me to sort it out

[BS-ryyj]

Great tutorial. So when is the next episode on GO enrichment expected to be available on your channel?

[amrsalaheldinabdallahhammo]

How to convert the Z-scores to significance to check if there is difference in significance between the cancer and normal values? and Does that Z-scores are one-tailed or two-tailed? Thanks a lot

[juangenomico]

Hello! How did you combine the multiple .txt files from Galaxy to put them into the Count Matrix? Thanks!

[Hadid]

I m looking for single cell analysis, do you have any course single cell RNA sequencing ?

[ProTech_]

Can you upload tutorial on comparing multi factor gene expression data genotype(control vs treated)

[manalalharbi]

Hi, I need someone explain this for me