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

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.

rna-seq next-gen r
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updated by Pin.Bioinf Pin.Bioinf • written by Gabby • Gabby

3 answers

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.

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written by jared.andrews07 jared.andrews07

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

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written by Gabby • Gabby

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

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written by jared.andrews07 jared.andrews07

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.

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written by archana.bioinfo87 archana.bioinfo87

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

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written by Pin.Bioinf Pin.Bioinf

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