HCL and Anova RNA-seq

Question

[kashyap_path10]

Hello, I don't have the background to use either R or Bioconductor. I have converted the RSEM to log scale. I would like to carry out HCL and one way anova. Could someone tell me if there is a software to do this that does not involve either R or Bioconductor ? Would it be possible to do it in MeV using the log2 data (I have previously used it for microarray data analysisand familiar with it) ? I saw that MeV has a RNA-seq module, but the input data requires counts/RPKM.

Thanks

Answer 1

[Michael]

Have your tried J-Express, it can do Anova, other options: SPSS, Matlab, Excel plugins. It's not necessarily easier than in R with these alternatives.

Note: such an analysis (ANOVA on log normalized counts instead of DEseq on raw counts) might not be considered state of the art.

Rather try to run DEseq2 through galaxy on your raw counts, e.g. on usegalaxy.org : https://usegalaxy.org/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fdeseq2%2Fdeseq2%2F2.11.38

Answer 2

[kashyap_path10]

Thank you. I will look into it.