Deciphering Life: One Bit at a Time
Compiling Against Python.h
How to make sure that cython can find python.h when using a self compiled python.
Project Consultation Template
What our labs project consult template looks like.
Heatmap Colormaps!
Examples of good colormaps to use for heatmaps, both divergent and incremental.
Recreating Correlation Values from Another Manuscript
Documenting my journey trying to recreate some correlations calculated in another manuscript.
Cairo and XQuartz in Mac GitHub Actions
Including cairo and xquartz in MacOS github actions
Dplyr in Packages and Global Variables
How to include dplyr in a package, and avoid warnings around global variables.
Pie Charts in RCy3
How to represent nodes as pie charts using Cytoscape and RCy3
Reusing ggplot2 Colors
When you want to reuse ggplot2 default colors across plots.
Migrating Self-Hosted GitLab Projects to GitHub
We wanted to migrate from self-hosted GitLab projects to GitHub repos. Here is some background on how we accomplished that.
Zooming GGraph Plots
Some code demonstrating how to zoom into portions of a ggraph.
R CMD Check and Non-PDF Vignettes
R CMD Check complaining about missing files? Here was my solution.
My Vacation in Barometric Pressure
What can we see from my phone's barometric pressure readings?
Random Forest Classification Using Parsnip
How to make sure you get a classification fit and not a probability fit from a random forest model using the tidymodels framework.
Coloring Dendrogram Edges with ggraph
Here is how I got edges colored in a dendrogram with ggraph. Use "node." in front of the node data column you want.
Keeping Figures in an Rmd -- Word Document
How to make your rmarkdown to word conversion also generate a directory of figures.
My Geographic Introduction
Adapting Piping Hot Data's Geographic Introduction animation for myself.
Proportional Error in Mass Spectrometry
Demonstrating the existence of proportional error in mass spectrometry measurements.
Highlighting a Row of A ComplexHeatmap
A simple way to highlight or bring attention to a row or column in a ComplexHeatmap.
Creating a Map of Routes Weighted by Travel
I made a map of my spouse's travel since we got Google phones for her birthday last fall. Here's how I did it.
Random Code Snippets
Introducing random-code-snippets.
Packages Don't Work Well for Analyses in Practice
I was wrong about using packages to structure statistical analyses. Also why I finally switched to {drake}.
Things I Learned About distill
The various things I learned about the distill blog setup while converting posts over from my old blogdown site.
Using group_by Instead of Splits
How to use group_by instead of split's to summarize things.
Narrower PDF Kable Tables
This is how you should make narrower kable tables in rmarkdown PDF documents.
Introducing Scientific Programming
How and when should we get people in academia programming? What if we had a unified front across the science labs?
Comments enabled via utterances
How I got utterances working on blogdown.
Comparisons using for loops vs split
for loops often hide much of the actual logic of your code because of all the necessary boilerplate of running a loop. split-ting your data can oftentimes be clearer, and faster.
Nicer PNG Graphics
Here are some tips for getting nicer graphics in your rmarkdown outputs.
Don't do PCA After Statistical Testing!
You might be tempted to do PCA after a statistical test. Read more to discover why this is a bad idea.
Finding Modes Using Kernel Density Estimates
Examples of finding the mode of a univeriate distribution in R and Python.
Split - Unsplit Anti-Pattern
Getting some speed using dplyr::join than my more intuitive split --> unsplit pattern.
Using IRanges for Non-Integer Overlaps
I wanted to make use of IRanges awesome interval logic, but for non-integer data.
Turn Robert's Beard Purple!
I'm trying to raise money for the Walk for Alzheimer's, will you sponsor me?
knitrProgressBar Package
Ever wanted a progress bar output visible in a knitr document? Now you can!
Licensing R Packages that Include Others Code
I wanted to include others code in my package, and couldn't find any good resources.
docopt & Numeric Options
Every input is a string in docopt. Every Input!!
Custom Deployment Script
I don't want to use Netlify for hosting, so I came up with this simple script to deploy my blog.
Differences in Posted Date vs sessionInfo()
If you see differences in the sessionInfo output and the date the post was published, this is why.
Linking to Manually Inserted Images in Blogdown / Hugo
This is my method to include something manually in a blogdown post.
I was Part of the Problem
Why do so many men think it's OK to lavish unwanted attention on women who don't want it?
Criticizing a Publication, and Lying About It
Critics of our last publication claimed we didn't make our data available, which is an outright lie.
Authentication of Key Resources for Data Analysis
NIH is asking for authentication of key resources. How does this apply to data analyses?
Random Forest vs PLS on Random Data
Comparing random-forest and partial-least-squares discriminant-analysis on random data to show the problems inherent in PLS-DA.
Novel Zinc Coordination Geometries
A bit of an explainer on our labs recent publication on finding and classifying zinc coordination geometries in protein structures.
Mouse / Human Transcriptomics and Batch Effects
A recent paper dug into some data from another paper, casting doubts on the first, all thanks to the data being available.
First Open Post-Publication Peer Review, with Credit!
A story about my first open peer-review.
Being a PhD Student and Post-Doc with Migraines
What it's like having migraines as a PhD student and PostDoc.
Travis-CI to GitHub Pages
How I automatically have some stuff get pushed to GitHub pages from a Travis CI job.
My Career Goals
I don't want to be a lab PI, but I want to stay in academia.
Analyses as Packages
Why I think packages make good ways to structure an analysis.
Creating an Analysis as a Package and Vignette
A walkthrough creating an analysis project as a package.
Packages vs ProjectTemplate
Why I think packages are better than the projectTemplate package.
Researcher Discoverability
Why do we need corporate products to enhance "researcher discoverability"?
Bioinformatics Presentations that Lack Results (or Biological Relevance)
Why do people have bionformatics presentations lacking relevance or results?
categoryCompare Paper Finally Out!
My first first author publication since starting my PostDoc is finally out, about my meta-annotation-enrichment software package categoyrCompare.
Self-Written Function Help
Do you want to be able to read function documentation for your own functions? Make your own package.
Installing MatLab vs Installing R
Personal frustrations around installing MatLab led to this particular rant.
Package Version Increment Pre- and Post-Commit Hooks
Two git commit hooks for incrementing the package version as part of commits.
Motivated Learning
Two personal stories on times I was very motivated to learn, as part of my Software-Carpentry instructor training.
PubmedCommons API
Pubmed commons is a new commenting system for pubmed articles.
Open vs Closed Analysis Languages
Talking about R & Python vs MatLab as examples of open and closed data analysis languages.
Pre-Calculating Large Tables of Values
Demonstrating a way to generate a large amount of numbers that otherwise might take a long time to calculate.
Portable, Personal Packages
My take on creating simple little packages for your own commonly used functions.
K-12 Wants Scientists!!
I recently attended a talk about PhD scientists in grade school teaching.
R, RStudio, and Release and Dev Bioconductor
Working with the development version of Bioconductor on linux can be a pain. This is one way to do it.
Reproducible Methods
A short missive on reproducibility, especially within computational work.
R Interface for Teaching
What is the best interface for teaching a language like R?
Tim Hortons Density
How far away are most Canadians from a Tim Hortons?
Storing Package Data in Custom Environments
How do you keep track of stuff for your own package without cluttering the users global space or setting a bunch of options?
Writing Up Scientific Results and Literate Programming
My thoughts on using literate programming to investigate and report scientific results
Writing Papers Using R Markdown
How I used RMarkdown to write a manuscript
Journal Club 2012-08-15
A summary of the paper Google Goes Cancer as was discussed in our journal club.
Creating Custom CDFs for Affymetrix Chips in Bioconductor
Examples of messing with Affymetrix CDF data in Bioconductor.