Final (?) to-do list

[catavallejos]

Adding this here as not everything has been documented in individual issues.

Note: 🔴 marks things that require changes in the BASiCS library.

• Revise abstract
• Revise introduction section. Particularly focus on intro to BASiCS paragraph. Yes, in general UMIs are preferable, but our model is not a NB distribution (we have two sources of over-dispersion). Also, UMI protocols tend to be sparser and some may not work well with BASiCS (e.g. snRNAseq).
• Run chains with EB prior -> in progress by @alanocallaghan
• Upload EB chains to gitlab
• Update workflow code to use EB chains
• Add EB option in param description for BASiCS_MCMC Add EB prior to main description of BASiCS usage #33
• Re-run chains with a seed and update seed in workflow.
• Add ref for EB. http://www.biostat.jhsph.edu/~fdominic/teaching/bio656/labs/labs09/Casella.EmpBayes.pdf
• Edit caption for dispersion-vs-mean figure. Grant information #37 ?
• Edit HVG/LVG to use threshold directly on epsilon ? 🔴 See Add EpsilonThreshold argument for DetectVG catavallejos/BASiCS#203
• Edit caption/size for figure plot-example-vg-naive. Potentially remove function.
• Current version removes diff over-dispersion testing as we want to encourage residual over-dispersion instead. If left like that, add a brief sentence to say that it's possible. OK?
• Look for another workflow to reference for GO analysis. https://f1000research.com/articles/5-1281/v3
• Edit caption and size for visualise-DE-plot plot. I tried, but the use of cowplot within BASiCS_PlotDE doesn't enable me to change some of the figure settings (e.g. legend text size). See Move from cowplot to patchwork  catavallejos/BASiCS#200 🔴
• Change plots in diff testing section to use denoised counts.
• Use a version of BASiCS_DenoisedCounts that excludes spike-ins 🔴. See Add option to exclude spike-ins from BASiCS_DenoisedCounts catavallejos/BASiCS#196 This is no longer needed.
• Update figs for diff variability testing. Heatmap temporarily stayed, but a better visualisation is required. Some high level intrerpretation needs to be writen.
• Review and update no-spikes section once EB chains are ready.
• Remove ESS from no-spikes section? We can just refer to what was done before.
• Add ref to 'stable genes' paper. See here. (guess you mean here)
• Remove uses of @ operator

[alanocallaghan]

chunk plot-example-vg-naive gives me a table of zero rows for LVG and HVG.

Fixed this. Not sure what the issue was but I increased the range of mean values.

[alanocallaghan]

Stable genes paper link gives me

Your session has timed out. Please go back to the article page and click the PDF link again.

(I added an updated link and the ref)

[alanocallaghan]

The spike vs no spike comparison looks awful now

[alanocallaghan]

Actually I think there was some caching going on. Seems okayish actually

[catavallejos]

That looks like what I saw :) On 9 Sep 2020, at 18:51, Alanocallaghan <[email protected]<mailto:[email protected]>> wrote: Actually I think there was some caching going on. Seems okayish actually [recached]<https://user-images.githubusercontent.com/10779688/92622119-9a9d6080-f2bc-11ea-90e3-7f4a5f8906e8.png> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#35 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABZJYNJEVE5R46LQFT3VBHDSE6P7VANCNFSM4P22ICWQ>. The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.