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Code should be broken down into small chunks that may be re-used.Write code for humans, write data for computers.Some recommendations for reproducible research Reproducible research can be repeated by other researchers with the same results.Vince Buffalo, author of Bioinformatics Data Skills (2015). “ Robust research is about doing small things that stack the deck in your favor to prevent mistakes.”.This kind of information is rarely available in scientific publications, but it’s now extraordinarly easy to put this kind of information on the web.Ĭould I replicate Figure 1 from your last publication? If not, what would you and your co-authors need to provide or do so I could replicate Figure 1 from your last publication?Īs scientists we should aim for robust and reproducible research

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What version of software / packages were used?.

Comments in the code / well-documented so a normal person can figure out how it runs.

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Only 4 used full 1000G workflow (realignment & quality score recalibration).

Only 10 used tools recommended by 1000G.

Only 19 were NGS studies with similar design.

299 articles published in 2011 citing the 1000 Genomes project pilot publication.

NGS: run-of-the-mill variant calling (align, process, call variants): 5.

Missing method/processing details (66%).

Missing software/hardware details (50%).

Nature also released a checklist, unfortunately with wimpy computational check (see #18).

We will examine statistics more closely and encourage authors to be transparent, for example by including their raw data.”

“ Nature and the Nature research journals will introduce editorial measures to address the problem by improving the consistency and quality of reporting in life-sciences articles… we will give more space to methods sections.

The Journal Nature on the issue of reproducibility: 3.

A reproducibility study in psychology found that only 39 of 100 studies could be reproduced.

Scientists in the United States spend $28 billion each year on basic biomedical research that cannot be repeated successfully.

Science is plagued by reproducibility problems.

(0 seconds) No need to look now, but don’t forget that the course help page has some useful resources on Markdown+RMarkdown.

Finally, browse through the RMarkdown Gallery. Continue reading through each section here on the navigation bar to the left ( Introduction through Cheatsheets, and optionally download and print out the cheat sheet). Click “Getting Started” and watch the 1 minute video on the Introduction page.

(10 minutes) See RStudio’s excellent documentation on Rmarkdown at.

Write a simple markdown document, and export it to HTML and/or PDF.

(5-10 minutes) Go to, an in-browser Markdown editor, and play around.

(5-10 minutes) Run through this 10-minute in-browser markdown tutorial.

(1 minute) Bookmark and refer to this markdown reference.

(30 seconds) Read the summary paragraph on the Wikipedia page.

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The resulting text file can be rendered into many downstream formats, like PDF (for printing) or HTML (websites).

All you really need to know is that Markdown is a lightweight markup language that lets you create styled text (like bold, italics, links, etc.) using a very lightweight plain-text syntax: (like **bold**, _italics_, (), etc.). Prior to class, spend a few minutes to learn a little bit about Markdown.

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