I've been dealing with gene-expression\gene-set analysis for about 6 years now, started with micro-arrays and recently RNAseq data, yet I still haven't found a convenient & reliable software to handle these tasks. I turn to you BioStars -perhaps you can point me at some neat tools I have been missing all these years? :)
The basic task I wish to conduct is to assess the statistical significance of changes to various custom gene-sets I input, clustering & graphical representation of the output is a nice bonus, but not a must.
These are some the tools I'm currently using:
# Genomica - Good old Genomica is piece of software, and does the job very nicely with hyper-geometric distribution! the only trouble is that's it's really outdated, and has lot's memory issues which makes it really hard to load large amount of data. Also, one cannot just copy-paste genesets, but have to go thought some laborious work to format the sets.
# GSEA - On first sight it looks like a winner, but I find it almost impossible to get it to run properly, and I simply hate formatting the input data (and the whole java interface).
# Expander - Seems promising, but not that intuitive to use (I was not able to download the most recent version).
Thanks for taking the time to read through, open to all suggestions.
P.S - please refer me to non-commercial software