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We need to download some raw sequence data in fastq format from GEO/SRA and run through an appropriate aligner (BWA, TopHat, STAR, etc) and then variant caller (Strelka, etc) or other analysis pipeline. How do we get started? First, we need the sequence data. Determine the SRR number and then... [Read More]

In a conda installation of R on a Linux machine, devtools::install_github fails because it is unable to find the correct system commands: $ docker run --rm -it condaforge/linux-anvil bash conda install -y r-base r-devtools unzip $ R -q -e 'devtools::install_github("r-lib/devtools")' > devtools::install_github("r-lib/devtools") Downloading GitHub repo r-lib/devtools@master from URL https://api.github.com/repos/r-lib/devtools/zipball/master Installation... [Read More]

This guide will take users through installation of R in a new Anaconda virtual environment. I always recommend biologists use Anaconda for managing R and its dependencies, because it gives us access to the Bioconda channel. The Bioconda channel is an incredibly powerful hub for many of the most important... [Read More]

You can write regular markdown here and Jekyll-theme will automatically convert it to a nice webpage. I strongly encourage you to take 5 minutes to learn how to write in markdown - it’ll teach you how to transform regular text into bold/italics/headings/tables/etc. [Read More]

Hi hi from Thien. This is my first post, how exciting!