Posted on Sat 04 May 2024 in how-to • Tagged with R, shiny, app, RNAseq, bioinformatics, data-visualization
How do you communicate results of an analysis? What tools do you use? Scientists that work in the wet lab are accustomed to firing up excel or some instrument-specific software and working with their own data. For genomics or other types of experiments in biology that result in large datasets …
Posted on Sun 21 April 2024 in how-to • Tagged with bioinformatics, data-visualization, rnaseq
One of the, if not the, most common downstream analysis task I'm asked to perform on RNAseq data is to generate the venerable "Volcano Plot." These are kind of the bioinformatics equivalent of saying "Hey! Look how much data I have!" Regardless, they are a pretty good way to quickly …
Posted on Sat 20 April 2024 in how-to • Tagged with sysadmin
Back in 2019, the halcyon days of yore, near the end of my time in graduate school I wrote a well-intentioned article about software management for multi-user linux systems (here). This original article was written based on my experiences as the de-facto sysadmin of our lab's bioinformatics server. I am …
Posted on Mon 19 August 2019 in how-to • Tagged with bioinformatics, python, workflows, snakemake
Over the past few years the use of workflow managers in genomics and bioinformatics has grown greatly. This is a great thing for the field and adds to our ability to perform reproducible analyses, especially for pipelines with many steps. These are common in bioinformatics, but prior to the use …
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 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 …