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Why hasn’t the field standardized around another tool? Is the list of excel plugins that something libreoffice couldn’t replace it, where they could just make a

Why hasn’t the field standardized around another tool? Is the list of excel plugins that something libreoffice couldn’t replace it, where they could just make add the options they need? My guess is the field is mostly lacking people interested in working on tooling like this?

pas 6y ago
Because actual quality (usability of research, open access, reproducibility, data availability, sane exposition/introduction, proper methods, documentation and code) is not as important as producing a fancy manuscript. Journals don't care, referees/reviewers might care, but they are unpaid and they usually don't want to rock the boat that much.
dnebdal 6y ago
It mostly has; most serious work is done in R and python, and there are a lot of supporting tools, documentation, and useful packages for both languages. It's not like the actual statistical analysis in your average paper was actually done in excel. However, Excel remains a nice tool for "I'll just look at this CSV with the final results from this analysis, sort it by correlation, and see if any of the usual suspects are up top". And if the next step is "yeah, that looks fine - I'll just copy the top 100 genes into this convenient GUI pathway analysis tool", you're suddenly exposed to whatever Excel did to your data. And as for "why not libreoffice", most researchers I personally run into are strong molecular biologists who've learned a subset of R for their uses; they're not really likely to go out and find libreoffice on their own. Besides, the writing process for papers includes sending drafts and spreadsheets to doctors and pathologists and editors, who are probably on hospital computers with a short whitelist of programs ... and I don't really want to debug subtle compatibility issues in the sort of garbage fire those documents can turn into.

pas 6y ago

Because actual quality (usability of research, open access, reproducibility, data availability, sane exposition/introduction, proper methods, documentation and code) is not as important as producing a fancy manuscript. Journals don't care, referees/reviewers might care, but they are unpaid and they usually don't want to rock the boat that much.

dnebdal 6y ago

It mostly has; most serious work is done in R and python, and there are a lot of supporting tools, documentation, and useful packages for both languages. It's not like the actual statistical analysis in your average paper was actually done in excel. However, Excel remains a nice tool for "I'll just look at this CSV with the final results from this analysis, sort it by correlation, and see if any of the usual suspects are up top". And if the next step is "yeah, that looks fine - I'll just copy the top 100 genes into this convenient GUI pathway analysis tool", you're suddenly exposed to whatever Excel did to your data. And as for "why not libreoffice", most researchers I personally run into are strong molecular biologists who've learned a subset of R for their uses; they're not really likely to go out and find libreoffice on their own. Besides, the writing process for papers includes sending drafts and spreadsheets to doctors and pathologists and editors, who are probably on hospital computers with a short whitelist of programs ... and I don't really want to debug subtle compatibility issues in the sort of garbage fire those documents can turn into.