Questions tagged [reproducibility]
The reproducibility tag has no usage guidance, but it has a tag wiki.
6
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How do I write tests for a snakemake pipeline?
I've been playing with snakemake, which is really powerful, however, I'd like to create a 'unit test' for the whole pipeline. e.g. a way to call the pipeline that tests that all the rules work ...
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1
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Replicate papers (beginner) [closed]
I have a strong mathematical and computer background (also with machine learning) and would like to switch to bioinformatics. I know a fair amount of biology. But I find it hard to find real world ...
- 111
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Details of ENCODE processing pipelines
I am trying to find details for how the ENCODE ChIP seq samples were processed.
Linking to a ChIPseq samples on www.encodeproject.org (e.g. https://www.encodeproject.org/experiments/ENCSR051DXE/) ...
- 3,241
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Lisp in bioinformatics
After many years of programming in Python, C/C++ and other mainstream languages, I am looking for a new language of pleasure, mainly as a part of mental hygiene. Since I really admire the ideas behind ...
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Ultimate reproducibility in R?
I'm looking for a convenient and reliable way to make an R analysis reproducible, either at different times or across collaborators.
Listing the package versions or a ...
- 2,594
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How to version the code and the data during the analysis?
I am currently looking for a system which will allow me to version both the code and the data in my research.
I think my way of analyzing data is not uncommon, and this will be useful for many people ...
- 2,705