Questions tagged [reproducibility]

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5 votes
2 answers
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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 vote
1 answer
93 views

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 ...
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  • 111
3 votes
1 answer
140 views

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/) ...
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7 votes
2 answers
251 views

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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  • 71
9 votes
4 answers
970 views

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 ...
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  • 2,574
27 votes
8 answers
1k views

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 ...
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