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.

Thanks heaps

You're literally asking other people to do the work for you? 

There's a user guide, which is pretty straight forward - http://www.bioconductor.org/packages/release/bioc/vignettes/cummeRbund/inst/doc/cummeRbund-manual.pdf

Hi,

There is a Nature Protocols paper which describes the analysis with cummeRbund, http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html

However if I see your experimental design, I would recommend edgeR for your analysis. It has a good manual, which is easy to understand for biologists.

Ben