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... The post Teaching an old bioinformatician new tricks appeared first on Dave Tang's blog ..read more

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... The post Downloading data from Zenodo using zenodo_get appeared first on Dave Tang's blog ..read more

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... The post Making precision medicine knowledge available for everyone appeared first on Dave Tang's blog ..read more

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... The post Domain and hosting renewed until 2026 appeared first on Dave Tang's blog ..read more

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... The post Check when install.packages fails in R appeared first on Dave Tang's blog ..read more

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)... The post Testing Singularity builds appeared first on Dave Tang's blog ..read more

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... The post Running RStudio Server with Singularity appeared first on Dave Tang's blog ..read more

Recently I have been learning about Singularity and have been experimenting with building Singularity images. However it seems that there is no layering in Singularity, which exists with Docker and Dockerfiles. This is quite convenient to have because building will resume from the point where the last step failed. However the comment: You can build... The post Building Singularity images in layers appeared first on Dave Tang's blog ..read more

ffq is a tool that can be used to fetch metadata from several data repositories. It can also be used to generate links to raw data hosted at the EBI (via FTP), AWS, GCP, and NCBI. I wrote a short Bash script called ffs that can generate the commands needed to download the raw data... The post Download from the SRA using ffq (and ffs) appeared first on Dave Tang's blog ..read more

I recently learned about code snippets in RStudio (ignore the strikethrough). As the name suggests, they are snippets of code that you can quickly insert into your source code in the source pane of RStudio. There are two ways to add code snippets: Click on the following: Tools -> Global Options -> Code -> Edit... The post TIL about code snippets in RStudio appeared first on Dave Tang's blog ..read more