Publications by quantixed
Step By Step: recreating a volcano plot in R
We have an analysis routine for proteomics data written for IgorPro. One output is a volcano plot. These plots show the fold change in one sample compared to another and plot that against a p-value to estimate how reproducible any changes observed are. This post is not about that software, but on the topic of how we can recreate this plot in R. Wha...
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Pledging My Time VI: scraping and analysis of race results in R
I’ve posted in the past about analysing race results in R (most recently here). I ran the 2023 MK Marathon and wanted to have a look at the finishing times. The days of race results being made available as a csv or xls for easy analysis seem to be behind us. Instead they tend to be served up on multiple webpages of 50 athletes’ results at a tim...
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Yet Another Movie: IMDB Top 250 movies
I’m not a big movie person. Nonetheless I have a media library with quite a few films in and I wondered how many “films to see before you die”-type movies I had in the collection, and how many were missing. I used R to find the answers. I’ve described previously how to get a plain text dump of a Plex database using WebTools-NG. I did that f...
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Probot: building a Mastodon bot
I have long admired albums2hear, a Twitter bot that posts albums. You can read a bit more about it here. There was no mastodon equivalent and so I decided to build one. You can follow the bot – currently called Albums Albums Albums (or AlbumsX3) – here. Idea behind the bot The idea is to periodically post an album. The toot is simple the artist...
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Form and File: estimating running form in R
There are lots of ways for runners and cyclists to analyse training data. A key question most fitness enthusiasts want to know is “how am I doing?”. “How you are doing” is referred to as form. Unsurprisingly, form can be estimated in many ways. One method is using training stress scores (acute training load and chronic training load) to a...
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Any Time At All: tweet frequency around the clock
Please consider this a “supplementary analysis” to my previous post looking at the frequency of tweets from my personal account over the last 12 years. I was curious about what times I was active on Twitter (measured by when I tweeted). Others might be interested in a solution to look at this in R. The code As in the previous post, we need to...
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Running Around: 2022 running dataviz in R
2022 was my best year for running to date. In 2021, my goal was to run 2021 km. For 2022, I wanted to see if I could run 2500 km and also to run 50 HM-or-more distance runs. I managed both and ended the year on a total of 2734 km. I also bagged two PBs for half marathon. Of course, if you subscribe to Strava or VeloViewer or whatever, you can get...
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Twitcher II: tweet frequency and top tweets
Another post looking at Twitter data in R. It follows this one and this one. I wanted to look again at my tweeting frequency over the 12 years on Twitter, but this time do it in a calendar view. Something like a GitHub commit calendar would be perfect. I have used a library for this in the past. Here, for no particular reason I used a function th...
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The Package: learning how to build an R package
I recently made my first R package and was asked how I did it. The answer of course was: I searched, read, and stumbled around until it was done. But having gone through the process I figured it was worthwhile summarising what I did and what I found tricky. First off, there are a ton of resources out there that describe how to go about building a...
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Tracking: announcing new R package TrackMateR
A short post to announce TrackMateR, a new R package to analyse TrackMate XML outputs. CodeInstructions Background TrackMate is a plug-in for ImageJ which ships with Fiji. It’s essential for single particle tracking work, particularly for microscopy movies. For example, tracking the movement of fluorescent vesicles inside cells. A tracking ses...
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