Tool for Time series data analysis

Question

[datanerd]

Hi All,

I have a time series data, with patients and normal at different ages. I would like to see a few expected trend with the gene expression over the ages and find the genes (1. they are different than normal, and they are increasing with age in the disease group.

I know MATLAB has a toolbox for it but was wondering if anyone knows of any good freely available software for it.

Thanks a lot!!

Mamta

Answer 1

[Charles Warden]

Yeah, you can do differential expression by specifying pairing between time points.

You can also play around with the 'timecourse' bioconductor package or EDGE.

Answer 2

[Devon Ryan]

You can do this with any of the common RNAseq differential expression packages, such as edgeR, DESeq2 and limma. I wouldn't recommend using MATLAB for something like this, you'll just be (likely poorly) reinventing the wheel.

[datanerd]

OK thanks. This is profiling data, so I am assuming limma should work. Will look into it!