Bioconductor - Githubissues

greenelab / computational-reagents

Rigor, Reproducibility, Transparency, and Reagent Validity for Computational Biologists

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Bioconductor #13

Open zz327 opened 7 years ago

zz327 commented 7 years ago

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. It helps - Everyone could download and re-run the program in R language;

It usually comes with test example and Reference Manual
Anybody who had problem with those package can submit a report and Bioconductor would directly contact the author of the package However, not all of the code are open source, which is quite disappointing.

linzho commented 7 years ago

I agree that Bioconductor is really useful - if paper writers would cite exactly what version of the package they are using and in what R version, and Bioconductor had one central place to locate all such versions, it would really help reproducibility

sklasfeld commented 7 years ago

I like the vignettes in for Bioconductor packages. Similar to Linda, I have found that many papers will just say we used "Diffbind" (a bioconductor package) and not explain what they did with the package, which version they used etc. Therefore, though bioconductor is nice for providing reproducible tools, it seems to not promote reproducibility.