Hi everyone,
I am not good at working with the R packages. I am looking for a user friendly and open access standalone tool (web or downloadable) for data normalisation, LIMMA analysis and PCA analysis? I used to use MEV4 but it keeps failing. Bioinformaticians are too busy :)
Thank you very much,
For open access data clustering visualization, I often recommend ClustVis. It's based on R/RShiny, but has a standard user interface that doesn't require knowing R yourself. It generates two main outputs, PCA and heatmaps. Visualizations are quite good, but you can also export the data to generate the plots elsewhere.
I cannot speak to data normalisation tools, as I don't know what data you're working with or what type(s) of normalisation you require or plan to apply. The only open access LIMMA I'm familiar with is in R, so no suggestions there either.
I'd suggest you take a look at NormalyzerDE (for normalisation);
http://www.quantitativeproteomics.org/
For PCA;
https://biit.cs.ut.ee/clustvis/
or
http://www.morpho-tools.net/index.html
Note that I have not used either of these two extensively and for general analysis InfernoRDN is great;
https://omics.pnl.gov/software/infernordn
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