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 Deployed website disconnects very frequently #11
• More reproducibility info? Deployed and local versions don't match More reproducibility info? Deployed and local versions don't match #12
• Simplify installation instructions Simplify installation instructions #13
• Explain in more detail the input TSV files Explain in more detail the input TSV files #14
• GO term and Selected tabs needs a bit more explanation GO term and Selected tabs needs a bit more explanation #15
• Improve selector for adjusted p-values cutoff
  Improve selector for adjusted p-values cutoff #16
• How to select all DE genes? How to select all DE genes? #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 < ***@***.***> wrote: Congrats on the pre-print! https://twitter.com/fellgernon/status/1034179967821725696 <https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_fellgernon_status_1034179967821725696&d=DwMCaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=64Z11d-nwokBqX9zZCLDgHbG760ek3NU0j9pxFxacQo&m=MQeLcOYg2Zt_75McKfr1y9gGP2FI33vKTjqIzbqzawY&s=kfPWG42TpbbRxCuPHdtmcGofZsyom_1zb1PyUcafs20&e=> — You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_UMMS-2DBiocore_debrowser_issues_18-23issuecomment-2D416362971&d=DwMCaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=64Z11d-nwokBqX9zZCLDgHbG760ek3NU0j9pxFxacQo&m=MQeLcOYg2Zt_75McKfr1y9gGP2FI33vKTjqIzbqzawY&s=tAkKTzWKrkWl-AQSPAjJYb24_WVwGmlkpjzNDq8RSqk&e=>, or mute the thread <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AEpOPOFCpUalfIBLV8e800q0JVORK4jEks5uVFqogaJpZM4H8AyP&d=DwMCaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=64Z11d-nwokBqX9zZCLDgHbG760ek3NU0j9pxFxacQo&m=MQeLcOYg2Zt_75McKfr1y9gGP2FI33vKTjqIzbqzawY&s=8ARg7ns72BalVGi9HhoRL6MgOWvw2dYYQUg7LwxpWCs&e=> .

-- Alper Kucukural, PhD BioCore Albert Sherman Center UMass Medical School 364 Plantation St. Worcester, MA 01605-4321 Lab: 508-855-3646