Prevent download errors in R by increasing the timeout

RDavo0

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)…

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Getting something to work once is not hard

reproducibilityDavo0

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,…

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What fraction of 10x reads map to ribosomal proteins?

single cellDavo0

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?

museDavo2

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

programmingDavo2

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

museDavo2

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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