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lcolladotor / derfinder

Annotation-agnostic differential expression analysis of RNA-seq data via expressed regions-level or single base-level approaches
http://lcolladotor.github.io/derfinder
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Can latest `derfinder` reproduce original (2013) analysis? #30

Closed brianhigh closed 9 years ago

brianhigh commented 9 years ago

Can the analysis in the paper Differential expression analysis of RNA-seq data at single-base resolution be reproduced using the latest version of derfinder? I ask because I am having a difficult time doing so using the "beta" version of the code and analysis_code.R. Thanks for any help you can provide.

lcolladotor commented 9 years ago

The software from the 2013 paper is different from this one as they use different statistical models. If you want to reproduce those results use https://github.com/alyssafrazee/derfinder

You can alternatively use this derfinder implementation to compare the results. Aka, replicate but not reproduce.