Radhika Khetani

\ \ \ \## plot using ggplot2 ggplot(melted_top20_sigOE) + geom_point(aes(x = gene, y = normalized_counts, color = sampletype)) + scale_y_log10() + xlab("Genes") + ylab("Normalized Counts") + ggtitle("Top 20 Significant DE...

The method listed above works nicely for html rendered markdown, looks a little funky without rendering.

Add a note about exonic deletions

With IGV

@karamveerverma37 thanks for the heads up. Lesson links have been updated, but lectures/slides are still not linked and probably won't be for a couple of months.

See figure 7 - https://journals.plos.org/ploscompbiol/article/figure/image?download&size=large&id=info:doi/10.1371/journal.pcbi.1005404.g007

Create a troubleshooting section at the end: - Look at err files if job is running - If jobs are pending, look at err and out files in `/n/groups/hbctraining/` Create...

In addition, when creating code chunks don't leave empty lines before and after the code: ### this is good: '''r something() ''' ### this is not: '''r something() '''

Finally, when adding links to the schedule add the relative path to the `.md` file. e.g. ../lessons/06_DGE_visualizing_results.md instead of https://hbctraining.github.io/DGE_workshop_salmon/lessons/06_DGE_visualizing_results.html

@marypiper , can you list a couple of examples here of how you want the code to be formatted? I can see this clearly when we are using pipes (%>%),...