How to make sure that cython can find python.h when using a self compiled python.
What our labs project consult template looks like.
Examples of good colormaps to use for heatmaps, both divergent and incremental.
Documenting my journey trying to recreate some correlations calculated in another manuscript.
Including cairo and xquartz in MacOS github actions
How to include dplyr in a package, and avoid warnings around global variables.
How to represent nodes as pie charts using Cytoscape and RCy3
When you want to reuse ggplot2 default colors across plots.
We wanted to migrate from self-hosted GitLab projects to GitHub repos. Here is some background on how we accomplished that.
Some code demonstrating how to zoom into portions of a ggraph.
R CMD Check complaining about missing files? Here was my solution.
What can we see from my phone's barometric pressure readings?
How to make sure you get a classification fit and not a probability fit from a random forest model using the tidymodels framework.
Here is how I got edges colored in a dendrogram with ggraph. Use "node." in front of the node data column you want.
How to make your rmarkdown to word conversion also generate a directory of figures.
Adapting Piping Hot Data's Geographic Introduction animation for myself.
Demonstrating the existence of proportional error in mass spectrometry measurements.
A simple way to highlight or bring attention to a row or column in a ComplexHeatmap.
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.
Introducing random-code-snippets.
I was wrong about using packages to structure statistical analyses. Also why I finally switched to {drake}.
The various things I learned about the distill blog setup while converting posts over from my old blogdown site.
How to use group_by instead of split's to summarize things.
This is how you should make narrower kable tables in rmarkdown PDF documents.
How and when should we get people in academia programming? What if we had a unified front across the science labs?
How I got utterances working on blogdown.
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.
Here are some tips for getting nicer graphics in your rmarkdown outputs.
You might be tempted to do PCA after a statistical test. Read more to discover why this is a bad idea.
Examples of finding the mode of a univeriate distribution in R and Python.
Getting some speed using dplyr::join than my more intuitive split --> unsplit pattern.
I wanted to make use of IRanges awesome interval logic, but for non-integer data.
I'm trying to raise money for the Walk for Alzheimer's, will you sponsor me?
Ever wanted a progress bar output visible in a knitr document? Now you can!
I wanted to include others code in my package, and couldn't find any good resources.
Every input is a string in docopt. Every Input!!
I don't want to use Netlify for hosting, so I came up with this simple script to deploy my blog.
If you see differences in the sessionInfo output and the date the post was published, this is why.
This is my method to include something manually in a blogdown post.
Why do so many men think it's OK to lavish unwanted attention on women who don't want it?
Critics of our last publication claimed we didn't make our data available, which is an outright lie.
NIH is asking for authentication of key resources. How does this apply to data analyses?
Comparing random-forest and partial-least-squares discriminant-analysis on random data to show the problems inherent in PLS-DA.
A bit of an explainer on our labs recent publication on finding and classifying zinc coordination geometries in protein structures.
A recent paper dug into some data from another paper, casting doubts on the first, all thanks to the data being available.
A story about my first open peer-review.
What it's like having migraines as a PhD student and PostDoc.
How I automatically have some stuff get pushed to GitHub pages from a Travis CI job.
I don't want to be a lab PI, but I want to stay in academia.
Why I think packages make good ways to structure an analysis.
A walkthrough creating an analysis project as a package.
Why I think packages are better than the projectTemplate package.
Why do we need corporate products to enhance "researcher discoverability"?
Why do people have bionformatics presentations lacking relevance or results?
My first first author publication since starting my PostDoc is finally out, about my meta-annotation-enrichment software package categoyrCompare.
Do you want to be able to read function documentation for your own functions? Make your own package.
Personal frustrations around installing MatLab led to this particular rant.
Two git commit hooks for incrementing the package version as part of commits.
Two personal stories on times I was very motivated to learn, as part of my Software-Carpentry instructor training.
Pubmed commons is a new commenting system for pubmed articles.
Talking about R & Python vs MatLab as examples of open and closed data analysis languages.
Demonstrating a way to generate a large amount of numbers that otherwise might take a long time to calculate.
My take on creating simple little packages for your own commonly used functions.
I recently attended a talk about PhD scientists in grade school teaching.
Working with the development version of Bioconductor on linux can be a pain. This is one way to do it.
A short missive on reproducibility, especially within computational work.
What is the best interface for teaching a language like R?
How far away are most Canadians from a Tim Hortons?
How do you keep track of stuff for your own package without cluttering the users global space or setting a bunch of options?
My thoughts on using literate programming to investigate and report scientific results
How I used RMarkdown to write a manuscript
A summary of the paper Google Goes Cancer as was discussed in our journal club.
Examples of messing with Affymetrix CDF data in Bioconductor.
If you see mistakes or want to suggest changes, please create an issue on the source repository.
Text and figures are licensed under Creative Commons Attribution CC BY 4.0. Source code is available at https://github.com/rmflight/researchBlog_distill, unless otherwise noted. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".