Find out which function is being used in R

Today I learned of the utils::getAnywhere() function in R, which I discovered when looking for a way to determine which function is going to be used when two attached packages have the same function name. I knew of base::search() which provides the search path used by R to look for objects (remember that everything in…

Continue Reading

Prevent download errors in R by increasing the timeout

If you find yourself getting a "Timeout of 60 seconds was reached" warning from download.file that’s preventing you from installing a package, you can increase the timeout in R by using options(). For example, when I was trying to run the following command: SeuratData::InstallData('ifnb') trying URL 'http://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.1.0.tar.gz' Content type 'application/octet-stream' length 413266233 bytes (394.1 MB)…

Continue Reading

Getting something to work once is not hard

As I wrote in a post on where to get information, I have been switching to offline resources such as books as a source of information. I’ve probably bought too many physical books as of late but I am reading them! One book that I’ve started to read is Clean Architecture by Robert C. Martin,…

Continue Reading

What fraction of 10x reads map to ribosomal proteins?

As you may have learned in school, ribosomes are cell organelles that can be thought of as protein factories because they aid in the synthesis of proteins. The eukaryotic ribosome is made up of ribosomal proteins and ribosomal RNA (rRNA). This post is about ribosomal protein gene expression and not non-coding rRNAs. I was interested…

Continue Reading

How and where to get information?

As you may have heard, Stack Overflow (SO) and OpenAI have recently announced a partnership, which basically just means allowing OpenAI to train models using data from SO and then selling these models. Kathy Reid summarised the problem perfectly: Like many other technologists, I gave my time and expertise for free to #StackOverflow because the…

Continue Reading

Naming variables and functions

An important aspect of programming that I never paid much attention to is the naming of things such as variables and functions. I think the reason is because a script/program will work as long as the syntax is correct and the naming of things is unimportant to the computer. When I first learned programming as…

Continue Reading

Teaching an old bioinformatician new tricks

The old adage is that you can’t teach an old dog new tricks because it is usually difficult to change people’s habits, traits or mindset. One reason may be because an "old dog" has done enough exploration and they want to exploit/reap the benefits of their previous ground work. They have dedicated a lot of…

Continue Reading

Downloading data from Zenodo using zenodo_get

From Zenodo’s Terms of Use page: Zenodo is an open dissemination research data repository for the preservation and making available of research, educational and informational content. Access to Zenodo’s content is open to all, for non-military purposes only. As stated on the main page, reasons for using Zenodo include: Safe — your research is stored…

Continue Reading

Making precision medicine knowledge available for everyone

I was recently contacted by the Stanford Deep Data Research Center at Stanford School of Medicine where they are working on "pioneering a transformative approach to precision medicine research and education." The center is led by Amir Bahmani who has made it his mission to make it possible for anyone to learn about bioinformatics and…

Continue Reading

Domain and hosting renewed until 2026

I just paid for another two years of web hosting for 324 USD (13.5 USD per month). I upgraded my account from a Business account (7.5 USD per month) to a Business II account, which is the same package but with a bit more storage. I upgraded my account because I decided I’m going to…

Continue Reading