To do by Sept 7 2020 - Githubissues

dburkhardt commented 4 years ago

Website

[x] Update contributing text with invitation to join CZI slack - @dburkhardt
[x] Flesh out website results page with metrics and full results - @dburkhardt
[x] Fix #43 - @dburkhardt
[x] Flip sort order

Tasks

[x] Pancreas #18
[ ] Tabula Muris #22 @M0hammadL
[ ] scArches #9 @M0hammadL
[x] Remove cheat / dummy methods

Longer term

[ ] Add zebrafish download from GEO #44 - @dburkhardt

scottgigante commented 4 years ago

@dburkhardt how are the website parts of this looking?

dburkhardt commented 4 years ago

@scottgigante I think the only thing left on the Website is to agree on a format for outputting results. Currently, the easiest thing would be for the output to be printed as TOML in files like https://github.com/singlecellopenproblems/SingleCellOpenProblems/blob/website/website/data/test.toml

[table]
  [[row]]
  data = ["Method", "kNN AUC", "MSE", "Paper"]
  [[row]]
  data = ["Procrustes", "0.00298303", "0.833141", "[Procrustes Methods in the Statistical Analysis of Shape]( https://www.jstor.org/stable/2345744)"]
  [[row]]
  data = ["Cheat", "0.0587961", "0" , "[Cheat](https://www.politifact.com/factchecks/list/?speaker=donald-trump&ruling=false)"]
  [[row]]
  data = ["MNN", "0.062768", "1.05657", "[Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors](https://doi.org/10.1038/nbt.4091)"]

This is different than what we had originally discussed, but I think it will be the best moving forward

scottgigante commented 4 years ago

Sure, sounds good. I'll make that change.

On Tue, 8 Sep 2020, 3:50 pm Daniel Burkhardt, notifications@github.com wrote:

@scottgigante https://github.com/scottgigante I think the only thing left on the Website is to agree on a format for outputting results. Currently, the easiest thing would be for the output to be printed as TOML in files like https://github.com/singlecellopenproblems/SingleCellOpenProblems/blob/website/website/data/test.toml

[table] [[row]] data = ["Method", "kNN AUC", "MSE", "Paper"] [[row]] data = ["Procrustes", "0.00298303", "0.833141", "Procrustes Methods in the Statistical Analysis of Shape"] [[row]] data = ["Cheat", "0.0587961", "0" , "Cheat"] [[row]] data = ["MNN", "0.062768", "1.05657", "Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors"]

This is different than what we had originally discussed, but I think it will be the best moving forward

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M0hammadL commented 4 years ago

@scottgigante I added muris_semis data loaders in a separate brunch but the build still fails and there is no clear error why this happens. Could you possibly check that?

dburkhardt commented 4 years ago

@M0hammadL the relevant error is here: https://travis-ci.com/github/singlecellopenproblems/SingleCellOpenProblems/jobs/384340310#L649.

openproblems-bio / openproblems

To do by Sept 7 2020 #47