Introduction to RNA-seqRNA-seq quantification: from reads to count matrix
RStudio Project and Experimental Data
Figure 1
![Your working directory should look like this](fig/02_setup/folders_working_dir.png)
Figure 2
![A new .Rproj file should be created in your chosen working directory.](fig/02_setup/rstudio_project.png)
Figure 3
![Your R working directory should now be set to where the .Rproj file resides.](fig/02_setup/rstudio_console.png)
Figure 4
![A file named GSE96870_counts_cerebellum.csv should now reside in the data folder.](fig/02_setup/data_folder.png)
Importing and annotating quantified data into R
Figure 1
Exploratory analysis and quality control
Figure 1
![](fig/04-exploratory-qc-rendered-unnamed-chunk-6-1.png)
Figure 2
![](fig/04-exploratory-qc-rendered-unnamed-chunk-7-1.png)
Figure 3
![](fig/04-exploratory-qc-rendered-unnamed-chunk-8-1.png)
Figure 4
![](fig/04-exploratory-qc-rendered-unnamed-chunk-9-1.png)
Figure 5
![](fig/04-exploratory-qc-rendered-unnamed-chunk-10-1.png)
Figure 6
![](fig/04-exploratory-qc-rendered-unnamed-chunk-11-1.png)
Differential expression analysis
Figure 1
![](fig/05-differential-expression-rendered-unnamed-chunk-8-1.png)
Figure 2
![](fig/05-differential-expression-rendered-unnamed-chunk-16-1.png)
Figure 3
Shrinkage of log fold changes is useful for visualization and ranking of
genes, but for result exploration typically the
independentFiltering
argument is used to remove lowly
expressed genes.
Figure 4
![](fig/05-differential-expression-rendered-unnamed-chunk-19-1.png)
Gene set enrichment analysis
Figure 1
![](fig/06-gene-set-analysis-rendered-unnamed-chunk-8-1.png)
Figure 2
![](fig/06-gene-set-analysis-rendered-unnamed-chunk-15-1.png)
Figure 3
Figure 4
![](fig/msigdb.png)
Figure 5
![](fig/06-gene-set-analysis-rendered-unnamed-chunk-48-1.png)
Figure 6
![](fig/06-gene-set-analysis-rendered-unnamed-chunk-50-1.png)
Figure 7
![](fig/06-gene-set-analysis-rendered-unnamed-chunk-50-2.png)
Figure 8
![](fig/06-gene-set-analysis-rendered-unnamed-chunk-55-1.png)
Figure 9
![](fig/06-gene-set-analysis-rendered-unnamed-chunk-56-1.png)
Figure 10
![](fig/06-gene-set-analysis-rendered-unnamed-chunk-57-1.png)
Figure 11
![](fig/06-gene-set-analysis-rendered-unnamed-chunk-59-1.png)
Figure 12
![](fig/simplifyEnrichment.png)
Next steps
Extra exploration of design matrices
Figure 1
![](fig/08-extra-design-rendered-unnamed-chunk-6-1.png)
Figure 2
![](fig/08-extra-design-rendered-unnamed-chunk-6-2.png)
Figure 3
![](fig/08-extra-design-rendered-unnamed-chunk-7-1.png)
Figure 4
![](fig/08-extra-design-rendered-unnamed-chunk-8-1.png)
Figure 5
![](fig/08-extra-design-rendered-unnamed-chunk-9-1.png)
Figure 6
![](fig/08-extra-design-rendered-unnamed-chunk-10-1.png)
Figure 7
![](fig/08-extra-design-rendered-unnamed-chunk-11-1.png)
Figure 8
![](fig/08-extra-design-rendered-unnamed-chunk-12-1.png)
Figure 9
![](fig/08-extra-design-rendered-unnamed-chunk-13-1.png)
Figure 10
![](fig/08-extra-design-rendered-unnamed-chunk-13-2.png)