Question: Tool for Time series data analysis
0
gravatar for Mamta
4.4 years ago by
Mamta410
United States
Mamta410 wrote:

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 alot!!

Mamta

ADD COMMENTlink modified 4.4 years ago by Charles Warden6.1k • written 4.4 years ago by Mamta410
1
gravatar for Charles Warden
4.4 years ago by
Charles Warden6.1k
Duarte, CA
Charles Warden6.1k wrote:

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

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

http://www.bioconductor.org/packages/release/bioc/html/timecourse.html

http://genomine.org/edge/index.html

ADD COMMENTlink written 4.4 years ago by Charles Warden6.1k
0
gravatar for Devon Ryan
4.4 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

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.

ADD COMMENTlink written 4.4 years ago by Devon Ryan88k

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

ADD REPLYlink written 4.4 years ago by Mamta410
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