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FlukeAndFeather / jese4sci-RC

Research Compendium track of the jese4sci short course
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RC101 #8

Closed Ronghao94 closed 2 years ago

Ronghao94 commented 2 years ago
  1. RStudio 2021.09.1, R 4.1.2, tidyverse 1.3.1, devtools 2.4.2, and rrtools 0.1.5
  2. A research compendium is a big package of all needed Information to let others reproduce and extend your data. Basically, It should contains a user manual, data, method, and output.
  3. The papers I participated, we had genetic data available, but the codes available upon requests (since most analyses used existing packages), and we did receive requests.
FlukeAndFeather commented 2 years ago

Basically, It should contains a user manual, data, method, and output.

The "user manual" part is a really good point. It's one thing to have all the materials in one place, but without a guide other scientists might not know how the parts fit together.

we had genetic data available

Were these in public databases?

the codes available upon requests

Were there any discussion in your research group(s) about making the code public?

elhazen commented 2 years ago

Also, what happens when a package is deprecated? How do we make sure the code will still work in a future-proof environment. @FlukeAndFeather have you ever heard of someone packaging their R version and package versions with code so that it could be run in the future without breakage?

Ronghao94 commented 2 years ago

Were these in public databases?

yes, NCBI GEO repository

Were there any discussion in your research group(s) about making the code public?

yes, but the bioinformaticians who helped us analyzing the data were reluctant to make all codes public, probably because they didn't think it was needed since no new packages were generated