Making precision medicine knowledge available for everyone
Dave Tang's blog
by Davo
3w ago
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
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Domain and hosting renewed until 2026
Dave Tang's blog
by Davo
3w ago
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
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Check when install.packages fails in R
Dave Tang's blog
by Davo
1M ago
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
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Testing Singularity builds
Dave Tang's blog
by Davo
1M ago
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
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Running RStudio Server with Singularity
Dave Tang's blog
by Davo
1M ago
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
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Building Singularity images in layers
Dave Tang's blog
by Davo
1M ago
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
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Download from the SRA using ffq (and ffs)
Dave Tang's blog
by Davo
8M ago
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
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TIL about code snippets in RStudio
Dave Tang's blog
by Davo
8M ago
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
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The tidyr pivot_longer and pivot_wider functions using base R
Dave Tang's blog
by Davo
8M ago
I use tidyverse packages a lot and most of the times I prefer them over base R functions, especially when it comes to plotting. However, sometimes I want to write an R script with no dependencies. This is typically referred to as using base R, i.e. using only functions that come with R. Theoretically this... The post The tidyr pivot_longer and pivot_wider functions using base R appeared first on Dave Tang's blog ..read more
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Deciding which bioinformatics tool to use
Dave Tang's blog
by Davo
9M ago
I just finished reading "Using prototyping to choose a bioinformatics workflow management system", which I summarised on Mastodon as follows: Enjoyed reading "Using prototyping to choose a #bioinformatics workflow management system". Paper describes authors' 10 day experience searching and implementing a workflow. Summary: Need to decide which tool to use? Shortlist a list of potentially... The post Deciding which bioinformatics tool to use appeared first on Dave Tang's blog ..read more
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