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…

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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…

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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…

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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…

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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…

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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…

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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…

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Check when install.packages fails in R

I recently found out that when install.packages() fails, it only returns a warning and not an error, i.e., the exit code is 0. R -q -e 'install.packages("thisdoesnotexist!!!")' > install.packages("thisdoesnotexist!!!") Installing package into ‘/home/dtang/R/x86_64-pc-linux-gnu-library/4.3’ (as ‘lib’ is unspecified) Warning message: package ‘thisdoesnotexist!!!’ is not available for this version of R A version of this package for…

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Testing Singularity builds

A quick post on testing Singularity builds, where I discovered how the %test section of the Singularity Definition File works. If you aren’t familiar, the Definition File is similar to the Dockerfile for Docker; it is used to define and build the image. From the documentation: A SingularityCE Definition File (or “def file” for short)…

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Running RStudio Server with Singularity

For running RStudio Server in a container, I’ve written about how to run RStudio Server with Docker; in the post I also listed out some reasons why you would want to do that instead of simply installing RStudio on your computer. This post demonstrates one way of running RStudio Server with Singularity. I learned that…

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