Links to packages and tools

There are a lot of great packages and tools being developed to help with reproducible research and data analysis. These are links to some we've seen and loved in the workshop.

D3 / Javascript for interactive graphics

Scott Murray's D3 tutorials and book

Eloquent Javascript book

CoffeeScript book

JSfiddle Great online tool for learning html/css/javascript. http://jsfiddle.net

R/qtlcharts, Karl Broman, Software for interactive graphics for quantitative trait locus mapping in experimental crosses; some tools have value more generally. http://kbroman.org/qtlcharts

Karl's other D3 examples https://www.biostat.wisc.edu/~kbroman/D3

Darin London's Docker Containerized Sequence Alignment

Using Docker and fig, you can rerun an alignment of Plasmodium raw data against a reference Plasmodium file. docker_bwa_aligner darin's docker registry

Here is an extension of the above that creates 'agents' that can run as daemons listening to a MongoDB for 'Tasks' to run. It extends the core bwa_aligner images to create new features, and images. mongo_agent_aligner

fig.sh Docker

Ideas for wrapping command-line docker commands as Mac OSX App

• Appify UI - "Create Mac apps. Use HTML5 for the UI. Script it with anything. Can not possibly be simpler." (Based on this script.)

• Also AppleScript: Example shell command called from AppleScript; you can save any AppleScript as an app.

• Instead of AppleScript, one can also use JavaScript. Here's an example

• Platypus [github] is more comprehensive than the above; includes the ability to make an installer.

• AppJS uses Node.JS.

Maker

• Repo
• What's wrong with make (IMO)
• Analysis with maker, vs with make

Organisation

• Carl Boettiger's template
• Lesson on project layout

Misc other tools

• ghwiki - very hacky helpers for working with a GitHub wikis to store project outputs.
• Notes from Jenny Bryan on the use of GitHub in a graduate course on data analysis, STAT 545 at UBC