Posted on Wed 17 July 2019 in how-to • Tagged with bioinformatics, data-science, r, python, big-data
Working with large amounts of tabular data is a daily occurance for both bioinformaticians and data scientists. There's a lot the two groups can learn from each other (great future post material). However, I recently ran into a situation that I was sure had to be relatively common. Apparently it …
Posted on Tue 09 July 2019 in commentary • Tagged with bioinformatics, thoughts, rnaseq, workflows
When analyzing RNAseq you're faced with many possible analysis pipelines. The biggest decision you need to make is what the purpose of your experiment is. I will make the assumption that most of the time people want to determine which genes are differentially expressed between two samples, genotypes, conditions, etc …
Posted on Fri 28 June 2019 in how-to • Tagged with bioinformatics, data-visualization
Last time we prepared our data using Deeptools.
Now we're going to do something kind of scandalous. R and python, living together in peace. What is this madness? I like R's ecosystem for manipulating data and plotting with the tidyverse. It still requires some tweaking, but with a bit of …
Posted on Thu 27 June 2019 in how-to • Tagged with bioinformatics, data-visualization
Commonly, in bioinformatics we're in the business of determining whether something, be it gene expression, or DNA methylation, or splicing, etc. is different between multiple conditions. Typically this would be done by comparing those data and using some kind of statistical test. However, with the continued advances in sequencing technologies …
When I started my Ph.D. I had a good amount of experience working in a Linux environment on my own computers. Mostly as a hobby. My advisor had bought a small server several years previous for a post-doc's project and I was offered this system to use for my …
Posted on Sat 15 June 2019 in how-to • Tagged with tutorial, pelican
In an effort to aid in my future job searching I decided I needed a personal/professional website. It needed to look good, contain links to my relevant social and job-search profiles, host some examples of work from my Ph.D. , showcase my skillset, and host my CV. GitHub pages …