Best pipeline for time course RNA-SEQ analysis for single cell organism

Question

[Gabby]

Hi As mentioned in the question, I would like to know, best pipeline till date for the RNA-Seq time course analysis. I have 3 biological replicates for 9 different time points (one condition), want to do differential expression analysis based on time points. Organism is a Eukaryote (Single cell).

If further detail needed to decide please let me know and also want to know, why particular pipeline can best best for this.

Answer 1

[jared.andrews07]

I don't know about 'best', but many common differential expression R packages can do this. DESeq2, limma, and edgeR are probably the most popular/well-regarded.

[Gabby]

Thanks, Can you please suggest any article related to my experiment conditions; means different biological replicates and time point.

[jared.andrews07]

Read the documentation for each of the respective packages. They all have sections devoted to time courses and setting the replicates is pretty easy.

Answer 2

[archana.bioinfo87]

Hi,

If your file size is not too big than you can try galaxy. Also, you can try any of these tools

https://gallery.shinyapps.io/DEApp/

http://renlab.org:3838/IDEA/#title1.2.

I think it may help you.

Answer 3

[Pin.Bioinf]

Try the Bioconductor package maSigPro , it is pretty easy to use.