-
Random Forest Analysis of Germfree Experiments
I’m using random forest models to make predictions on the “humanized” germfree mouse experiments.
-
Time Series Analysis
In this post I outline some methods for analyzing time-series multivariate data or “compositional time-series data”. This will be important for both the germfree study and the C. difficile dynamics paper.
-
Germfree Cage Summaries
Summaries, showing the overview of each cage, have been generated using the “build_CageSummaries.R” and “build_microbiotaSummaries.R” files. These include mouse weight change, C. difficile CFU, and microbiota changes over time.
-
16S Total Relative Load
Progress updates on the qPCRs for assessing total 16S relative load for the antibiotic treatments I’ve administered. Original Post 6/19/15
-
Toxin Assay Progress
Progress updates on the toxin assays for the “Human-derived gnotobiotic murine models of CDI”. The paper title is a work in progress! Original Post 6/18/15
-
Justification of Toxin Assay Samples
Deciding on the number and which samples to be assessed for C. difficile toxin levels.
-
Overview of the Humanized GF C. difficile Project
Main question: How does the microbiota affect not only colonization of C. difficile but also the course of infection?
-
DANG Meeting R
Notes from the last DANG meeting.
-
Results Section: Tables and Figures
List of things working on for current paper tables and figures. Original Post: 2014-11-21
-
Markdown Resources
A list of Markdown resources.
-
Writing Resources for Grad School
List of resources online for writing, whether for a research article, grant, or for dissertation.
-
Software Carpentry Workshop Notes
Notes from the Intermediate room at the workshop.
-
Variable Selection for Models
Web resources for variable selection in linear models.
-
Personal Scripts Github Repository
OMG I’m implementing Pat’s suggestions.
-
Results Section Progress
Updates on Results Section for Day 0 Colonization Paper.
-
Computer Crash
This is a friendly reminder to BACK UP YO SHIT.
-
It's FriYAY
That is all.
-
First Blog Post
Woo look at me writing my first blog post!
-
What is the purpose of this blog?
How frequently do you update your lab notebook? Do you have a notebook for working on the computer? What is the point of a lab notebook even? How dependent are you on tools that utilize a graphical user interface (GUI)? If you were asked to regenerate a figure from your last lab meeting, how long would it take? We will be using blog posts as a way to maintain an electronic lab notebook in conjunction with project-specific GitHub repositories for our bioinformatics analyses.
-
Best practices
Let’s discuss and be open to evolving a set of best practices for fostering an reproducible environment for doing microbial informatics.
-
Customizing your blog
You should notice by now that there’s a lot of awesomeness on our blog even though you haven’t done anything yet. Although you are awesome, you aren’t really - that - awesome. Let’s bring you down to earth…
-
Setting up Disqus
A widely used tool for commenting on blogs and websites is Disqus. Go ahead over there and in the upper right corner of the page click the “Sign Up” button. Go through the registration steps and then hurry back here and we’ll get started with adding Disqus to your blog.
-
kntir demonstration
You can generate blog posts using the knitr R package. Don’t be fooled, even though it is an R package, it allows one to run commands in Python and bash. Before you get going in knitr, be sure to see the Resources page for tutorials on how to use knitr.
subscribe via RSS