I have a list of identified phosphopeptides by proteome discoverer between three different conditions. I would like to compare their sequences to get information about peptide hydrophobicity, acidity, legth... between the conditions, as well to see what amino acids are sorrounding the phosphosite.
Are there any good R packages or scripts that do these analysis and give good data visualization for this purpose?
Thanks
I am not really sure about yout data structure, but principal component analysis (PCA) or heatmap representation of your data could help you. PCA is included in many packages in R (just try to find), and also some packages are dedicated to heatmap drawing ( for example pheatmap package).
Hi Ignacio Arribas Díez ,
You can try online tools such as Plotly (https://plot.ly/r/) and ClustVis (https://biit.cs.ut.ee/clustvis/) for such analysis.
Varsha
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