I have biology background and am just starting to learn Rstudio. I have made the database from the cuffdiff output from cufflinks. But now I need to visualize the data and get to meaningful figures for publications.
I have installed cummeRbund but I have zilch programming skills and am unable to understand the commands.
I need someone to help me by writing full analysis script for the following samples.
I have three strains and one wildtype grown at two different temperatures 16C and 23C. I am looking for differentially expressed genes, isoforms, TSS..
I also need separate graphs for each isoform and their expression level (I know Sashimi in IGV is goo but it doesnot give me what I want i.e., separate quantification of each isoform).
What other analysis is possible? heatmaps.. etc.