Deciphering Life: One Bit at a Time

My Geographic Introduction

maps
graphing
visualization
animation

Adapting Piping Hot Data's Geographic Introduction animation for myself.

Proportional Error in Mass Spectrometry

mass-spectrometry
proportional-error
omics
metabolomics

Demonstrating the existence of proportional error in mass spectrometry measurements.

Highlighting a Row of A ComplexHeatmap

random-code-snippets
heatmap
visualization

A simple way to highlight or bring attention to a row or column in a ComplexHeatmap.

Creating a Map of Routes Weighted by Travel

graphing
maps
visualization

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

random-code-snippets

Introducing random-code-snippets.

Packages Don't Work Well for Analyses in Practice

R
development
packages
vignettes
programming
analysis
workflow

I was wrong about using packages to structure statistical analyses. Also why I finally switched to {drake}.

Things I Learned About distill

distill
blogdown
rmarkdown

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

R
dplyr
split
group-by
programming
development

How to use group_by instead of split's to summarize things.

Narrower PDF Kable Tables

R
knitr
kable
learning
rmarkdown

This is how you should make narrower kable tables in rmarkdown PDF documents.

Introducing Scientific Programming

R
reproducibility
programming
academia

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

blogdown
commenting
utterances

How I got utterances working on blogdown.

Comparisons using for loops vs split

R
for-loop
split
purrr
development

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!

pca
bioinformatics
R
t-test

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

R
python
kernel-density
pdf
probability-density
programming

Examples of finding the mode of a univeriate distribution in R and Python.

Split - Unsplit Anti-Pattern

R
development
programming
purrr
dplyr
join

Getting some speed using dplyr::join than my more intuitive split --> unsplit pattern.

Using IRanges for Non-Integer Overlaps

R
iranges
development
programming

I wanted to make use of IRanges awesome interval logic, but for non-integer data.

Turn Robert's Beard Purple!

alzheimers
fundraising

I'm trying to raise money for the Walk for Alzheimer's, will you sponsor me?

knitrProgressBar Package

packages
R
development

Ever wanted a progress bar output visible in a knitr document? Now you can!

Licensing R Packages that Include Others Code

R
packages
open-science
licensing

I wanted to include others code in my package, and couldn't find any good resources.

docopt & Numeric Options

R
development
programming
docopt

Every input is a string in docopt. Every Input!!

Custom Deployment Script

R
blogdown
development
random-code-snippets

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()

development
blogdown

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

hugo
R
blogdown

This is my method to include something manually in a blogdown post.

I was Part of the Problem

metoo
academia

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

publications
peer-review
zinc
academia

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

reproducibility
open-science
analysis

NIH is asking for authentication of key resources. How does this apply to data analyses?

Random Forest vs PLS on Random Data

random-forest
machine-learning
partial-least-squares
statistics
analysis

Comparing random-forest and partial-least-squares discriminant-analysis on random data to show the problems inherent in PLS-DA.

Novel Zinc Coordination Geometries

zinc
structural-biochemistry
open-science
reproducibility
visualization
publications

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

open-science
transcriptomics
batch-effects
publications
peer-review

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!

open-science
peer-review
publications

A story about my first open peer-review.

Being a PhD Student and Post-Doc with Migraines

phdisabled
migraines
academia

What it's like having migraines as a PhD student and PostDoc.

Travis-CI to GitHub Pages

R
reproducibility
travis-ci
github
publishing

How I automatically have some stuff get pushed to GitHub pages from a Travis CI job.

My Career Goals

post-doc
career
academia

I don't want to be a lab PI, but I want to stay in academia.

Analyses as Packages

R
development
packages
vignettes
programming
analysis

Why I think packages make good ways to structure an analysis.

Creating an Analysis as a Package and Vignette

R
development
packages
vignettes
analysis
programming

A walkthrough creating an analysis project as a package.

Packages vs ProjectTemplate

R
packages
analysis
development

Why I think packages are better than the projectTemplate package.

Researcher Discoverability

github
open-science
academia
research

Why do we need corporate products to enhance "researcher discoverability"?

Bioinformatics Presentations that Lack Results (or Biological Relevance)

bioinformatics
academia
research

Why do people have bionformatics presentations lacking relevance or results?

categoryCompare Paper Finally Out!

R
bioconductor
meta-analysis
publications
git
github
open-science
visualization
annotation-enrichment

My first first author publication since starting my PostDoc is finally out, about my meta-annotation-enrichment software package categoyrCompare.

Self-Written Function Help

R
packages
documentation
development
devtools
roxygen2
docstrings

Do you want to be able to read function documentation for your own functions? Make your own package.

Installing MatLab vs Installing R

MatLab
R

Personal frustrations around installing MatLab led to this particular rant.

Package Version Increment Pre- and Post-Commit Hooks

R
git
packages
development
programming
random-code-snippets

Two git commit hooks for incrementing the package version as part of commits.

Motivated Learning

learning
software-carpentry
git
calculus

Two personal stories on times I was very motivated to learn, as part of my Software-Carpentry instructor training.

PubmedCommons API

open-science
pubmed

Pubmed commons is a new commenting system for pubmed articles.

Open vs Closed Analysis Languages

open-science
R
python
MatLab
programming
development

Talking about R & Python vs MatLab as examples of open and closed data analysis languages.

Pre-Calculating Large Tables of Values

R
pre-calulations
programming
development
c++

Demonstrating a way to generate a large amount of numbers that otherwise might take a long time to calculate.

Portable, Personal Packages

R
packages
development

My take on creating simple little packages for your own commonly used functions.

K-12 Wants Scientists!!

post-doc
academia
science
teaching

I recently attended a talk about PhD scientists in grade school teaching.

R, RStudio, and Release and Dev Bioconductor

R
bioconductor
rstudio
programming
packages
development

Working with the development version of Bioconductor on linux can be a pain. This is one way to do it.

Reproducible Methods

open-science
reproducibility
bioinformatics

A short missive on reproducibility, especially within computational work.

R Interface for Teaching

R
teaching
notebooks

What is the best interface for teaching a language like R?

Tim Hortons Density

R
mapping
tim-hortons

How far away are most Canadians from a Tim Hortons?

Storing Package Data in Custom Environments

R
packages

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

literate-programming
academia
notebooks
reproducibility

My thoughts on using literate programming to investigate and report scientific results

Writing Papers Using R Markdown

R
open-science
reproducibility
literate-programming
rmarkdown

How I used RMarkdown to write a manuscript

Journal Club 2012-08-15

journal-club

A summary of the paper Google Goes Cancer as was discussed in our journal club.

Creating Custom CDFs for Affymetrix Chips in Bioconductor

R
bioconductor
bioinformatics
cdf
affymetrix
microarray
random-code-snippets

Examples of messing with Affymetrix CDF data in Bioconductor.

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Deciphering Life: One Bit at a Time

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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 ...".