Which online open source applications are best to use for analysis of microarray data?

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Pawel Buczkowicz

R is a good option for open source analysis tools of a wide variety of data. If you were using GeneSpring I'm assuming you may want to analyze Agilent array data. There are specific packages for different Agilent arrays, such as https://www.bioconductor.org/packages/release/bioc/html/agilp.html, https://www.bioconductor.org/packages/3.5/bioc/html/AgiMicroRna.html and https://www.bioconductor.org/packages/3.5/bioc/html/LVSmiRNA.html to name a few.

Ragavendrasamy Balakrishnan

Limma package in R software is good.

Pranavathiyani G.

You can have a look at NCBI's GEO2R.

https://www.ncbi.nlm.nih.gov/geo/geo2r/