Question: Best pipeline for time course RNA-SEQ analysis for single cell organism
0
gravatar for thindmarsmission
6 months ago by
thindmarsmission0 wrote:

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 • 466 views
ADD COMMENTlink modified 6 months ago by Pin.Bioinf240 • written 6 months ago by thindmarsmission0
2
gravatar for jared.andrews07
6 months ago by
jared.andrews071.9k
St. Louis, MO
jared.andrews071.9k wrote:

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.

ADD COMMENTlink written 6 months ago by jared.andrews071.9k

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

ADD REPLYlink written 6 months ago by thindmarsmission0

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

ADD REPLYlink written 6 months ago by jared.andrews071.9k
2
gravatar for archana.bioinfo87
6 months ago by
archana.bioinfo87100 wrote:

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.

ADD COMMENTlink modified 6 months ago • written 6 months ago by archana.bioinfo87100
2
gravatar for Pin.Bioinf
6 months ago by
Pin.Bioinf240
Malaga
Pin.Bioinf240 wrote:

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

ADD COMMENTlink written 6 months ago by Pin.Bioinf240
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