The best tool for time course differential expression with R

Question

[sabaghianamir70]

Hello

I want to analyse some time series data

I have been tried with galaxy but i think the tool is not useful enough.

So i want to get my count data into R studio and get my DEG from there. But i dont know what is the easiest and best package for that. I dont think this can be done with limma or Deseq2 or EdgeR. I did this with Deseq2 before, for example differentiated the time point 0 with time point 1 and then time point 0 with time point 2,

0 with 1
0 with 2 
0 with 3
And so on.

But i think this is not the correct way.

Answer 1

[Kristoffer Vitting-Seerup]

Appart from ATpoint's suggestion I can recommend voom-limma IF you have many timepoints since they allow for modeling via splines. You can take a look in section 9.6 (p 47) of the limma vignette (9.6.2 for the spline modeling).

Answer 2

[ATpoint]

Time-series experiments are covered in DESeq2 manual: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#time-series-experiments

which eventually refers to their RNA-seq workflow: http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#time-course-experiments

which you might want to check out.