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Comment: How to combine two DESeq2 objects (dds) for analysis
Hello Luke, Since DESeq2 takes raw counts, and provided that you only have the DESeq objects, you can extract raw counts with ```r count_…
Comment: deseq2 normalized counts as an input to deseq2
Hi Michael, I have a similar question regarding the normalization of my RNAseq data. I used VSN normalization on pre-filtered data as f…
Comment: Annotated dendogram (tree) from tbl_graph
Thx, actually I have started reading it and think at some point I'll get it. However, I was looking for something that would not need me …
Comment: pathview: Warning: Failed to download KEGG xml/png files, hsa04110 skipped!
Really appreciate your help :) At last, I can fix my problem. I have learned to check my code.
Comment: how can I do gene differential analysis on data after vst
I advised you to use limma-trend, which you can look up in the limma User's Guide. You simply analyse the vst values as if they were from a…
How many parameters should be included in the model design for deseq2?
Answer: Failed to install Biobase
Answer: Latest version of ggtree (3.6.2) unavailable on Anaconda. Only 3.6.0 exists.
BiocGenerics package: 404 error during R shiny app deployment
Comment: does anyone how to create rarefaction curves from a phyloseq object?
James W. MacDonald
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