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Jeremy Chacon

Articles by Jeremy Chacon:

My 10 Favorite R Packages and the Cool Things You Can Do with Them

One of the best parts of R is how extensible it is. Over the years, the community has put together hundreds (thousands?) of amazing packages to make your workflow easier. The downside of this wealth is that it can be hard to find packages that do exactly what you want! Therefore, I’ve put together a…

02 Feb 2015 Software and Online Tools

An Easy Way to Start Using R in Your Research: Making Pretty Plots With ggplot

The thing that was most difficult for me as an R beginner was plotting graphs with error bars – there is no concise way to do this with base graphics. There are workarounds, often using the ‘arrows’ command, but isn’t there a simpler way? Yes, in fact there are a handful of plotting packages for…

30 Jul 2014 Lab Statistics & Math

R You Ready? Using R for Statistical Tests

We’ve been slowly coaxing you along in our R tutorials.  We’ve introduced what R is, gave you a basic tutorial into how to use R and also spent some time learning how to explore your data with R. By now you are probably itching to use R for more complicated analyses.  To indulge you, I…

16 Jun 2014 Lab Statistics & Math

An Easy Way to Start Using R in Your Research: Exploratory Data Analysis

As you’ve probably kind of guessed from our previous articles Introducng R and the Basic R Tutorial, we think R programming language and R-studio are great tools for data analysis and figure production.  And now we are about to prove it! So, you’ve collected some data and are pretty sure you know what statistical test…

21 Apr 2014 Lab Statistics & Math

The lac Operon as a Microscopy Tool

The lac operon is an amazing tool in molecular biology.  It has been used for decades to turn on protein expression in an inducible manner with IPTG. The result is synthesis of vast amounts of protein to be used as you wish. While the lac operon is an amazing tool for protein production, it is…

08 Jan 2014 Microscopy and Imaging

Show Us Your Moves: Making an MSD Plot

In the previous article, I showed you how to interpret mean-squared displacement (MSD) and showed four easy things you can learn from an MSD graph at a quick glance. Now let’s turn from analyzing an MSD plot to making one. I am going to use the programming language R to generate simulated data and then…

06 Nov 2013 Lab Statistics & Math

How Does it Move? Interpreting Motion of an Object with the Mean-Squared Displacement

Stuff moves. It is useful to study how stuff moves, because motion analysis can tell us a lot about the object that is moving. For example, we can learn if an object’s motion is aimless, diffusive wandering, or directed towards some goal, free to explore the available environment, or restricted to a confined space. Studying…

28 Oct 2013 Lab Statistics & Math

An Easy Way to Start Using R in Your Research: Basic Tutorial

So now you’re convinced that R is the language for you, you’ve downloaded R-Studio (from http://www.rstudio.com/)  and opened it, and. . .what the hell do you do now? Great question! I always find it easiest to learn by doing something, rather than just by seeing a list of possibilities, so here I’ll walk you through…

14 Aug 2013 Lab Statistics & Math
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