San Diego State University Gene Expression Dataset Computer Programming Task
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Now that you have a brief overview of RNA-seq analysis and one of the most popular bioinformatics software available, DESeq2, you will conduct your own demo analysis in order to get a sense of the entire process.
Use the DESeq2 tutorial to recreate the analysis with one of the following data sets: attached below
For submission, upload a DESeq2 results table in “.csv” format, with entries sorted by descending Log2FoldChange values and entries with adjusted p-value (padj) <0.075 removed. Please make make sure to annotate your “.rmd” document with what each function/tidbit of code is doing; you will be uploading this R markdown document as part of your notebook check 3.
For your third notebook check, please upload your R Markdown (.rmd) document which you used for your personal differential gene expression analysis assignment. Make sure to annotate/take notes in the markdown format (#take your notes like this) on what each function and section of the tutorial/assignment is doing.
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