Initial impression, great work!

[lcolladotor]

Hi,

I just looked at debrowser and I think that it's a great idea. It could be specially useful for teaching how to do RNA-seq data analysis without teaching R commands or for researchers that want to explore their DE results.

I found a list of technical issues or things I believe could be improved, see:

• Deployed website disconnects very frequently https://github.com/UMMS-Biocore/debrowser/issues/11
• More reproducibility info? Deployed and local versions don't match https://github.com/UMMS-Biocore/debrowser/issues/12
• Simplify installation instructions https://github.com/UMMS-Biocore/debrowser/issues/13
• Explain in more detail the input TSV files https://github.com/UMMS-Biocore/debrowser/issues/14
• GO term and Selected tabs needs a bit more explanation https://github.com/UMMS-Biocore/debrowser/issues/15
• Improve selector for adjusted p-values cutoff https://github.com/UMMS-Biocore/debrowser/issues/16
• How to select all DE genes? https://github.com/UMMS-Biocore/debrowser/issues/17

I submitted them as independent issues so it'll be easier for you to track/address them.

Also note that you use DESeq in several parts of the app and the documentation when you really mean DESeq2. These are different packages so I would just encourage you to be crystal clear.

Thinking on the long run, you might want to explore using https://github.com/aoles/DEFormats (cc'ing @aoles) if you want to support multiple differential expression packages.

Overall, this is great work and I know that you just submitted your package to Bioc. I hope to see debrowser at Bioconductor for a long time.

Best, Leo

Leonardo Collado Torres, PhD Candidate Department of Biostatistics Johns Hopkins University Bloomberg School of Public Health Website: http://lcolladotor.github.io/about.html

[nephantes]

Thanks Leonardo, I will be addressing your comments pretty soon in the new version.

[lcolladotor]

Congrats on the pre-print!

https://twitter.com/fellgernon/status/1034179967821725696

[nephantes]

Thanks Leonardo. Hope the paper will be accepted soon. Best, Alper

On Mon, Aug 27, 2018 at 4:46 PM Leonardo Collado-Torres < notifications@github.com> wrote:

Congrats on the pre-print!

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