Regtools is a handy program that can investigate gene expression regulation by focusing on mutations identified in either DNA or RNA sequencing data (1). It can also produce files required for other pipelines, like Sierra that I am currently using, such as a splice junctions file (2). While the GitHub readme presents a simple installation guide for this package, I found unique challenges in installing the program on a Unix-based server. This article details how to install the program in this particular environment.

The beginning of the installation is using provided code from the regtools GitHub directly (1):

### Code…

There are many valuable tools in R for data science. Recently, I have been using LDLinkR to gather linkage disequilibrium statistics for my research. What I quickly discovered is that this algorithm can only process a maximum of 1,000 SNPs per iteration. Given that data is outputted as a data frame, I am left with several disjointed data frames that I want to combine to form a single data frame required for my pipeline. This can be visualized by the following where I want to combine the smaller squares into a larger square:

There are many valuable tools for a research scientist in genetics. One such tool is the Integrative Genomics Viewer. This program has several functions useful for someone looking at sequencing data. I will be going over a focused function for one seeking to grab select data quickly.

Homozygous or Heterozygous?

Heterozygosity has implications on physical traits and the strength of a harmful effect. Inspecting for this is fortunately relatively easy. After loading a genome file, zoom into your desired locus by entering the locus into the bar at the top of the screen:

It has been unfortunate that there has been so much misinformation about the life-saving COVID-19 vaccines. The vaccine is the best way to prevent death from COVID-19, a genuine possibility (at least 5 people in 100) if one gets infected and is not vaccinated. Overall, its side effects are minimal and reasonable, considering that it prevents me from dying from the virus. This is a brief recount of my experience receiving my second vaccine. I am fully transparent with the side effects that I experienced.

When I went to the vaccine distribution site with my wife, there was not much…

I recently read an article from the Montreal Gazette documenting protests against COVID-19 restrictions, including a curfew. Comments raised beliefs that not wearing masks and obeying restrictions was an act of courage and exercising freedoms. Below is the statement that I made about such actions.

MD and COVID-19 researcher here. I’m afraid I have to disagree with commenters suggesting that a refusal to wear masks and obey restrictions is a ‘courageous exercise of freedom.’ The pandemic has gone on for over a year. Millions have gotten sick and died, which included many in the United States who were exercising such…

It feels like COVID-19 has been going on for a long time because it has, and the inconveniences become increasingly annoying every day. Fortunately, a greater proportion of the international population is vaccinated, and more progress is being made towards herd immunity. I summarize here points that I have made while fighting COVID misinformation online, given that these are thus the questions that most concern us at this point.

Does the vaccine protect me against the new variants?

The vaccine still has effectiveness against the new variants. True, you can still be infected while vaccinated, but being vaccinated prevents you…

Protests against COVID-19 policies have persisted throughout the pandemic. I can understand wanting life to be back to normal, visiting friends and family, and doing something as basic as going to a restaurant with my wife. As a physician, I am disturbed that such protests often perpetuate falsehoods about the pandemic, such as it not being real, it being no worse than the flu, and the number of dead is inflated or similar compared to other years. I find the last the most egregious as it suggests that all of those we have lost did not matter.

I have been…

There is a lot of misinformation regarding COVID-19 vaccines. I have written multiple articles on my Medium page documenting the objective aspects of COVID-19, including vaccine side effects. Yesterday, I was fortunate to receive my COVID-19 vaccine as some researchers had the opportunity to sign up for it.

I flowed through the registration at the vaccination center relatively quickly. As with every other medical procedure, I was appropriately asked for contraindications to the vaccine (have I had reactions to vaccines in the past). The center exists so people who have severe reactions can be cared for (a stretcher in a…