Preserving institutional knowledge

R Tips: Here package

Download the Rmd file Introduction If someone were to ask me: “Quick - give me a useful R package. Go!” I would respond with the here package. The problem I’ve been in the position where I am running R code on both Windows and Linux or even reusing a script in a different project. I was in the bad habit of using absolute paths and this made transitioning from Linux to Windows a huge pain.

Using SRA toolkit

Getting started with the SRA Toolkit Let’s say you want to download some sequences from the sequence read archive (SRA) at NCBI. How do you do it? First, we need to make sure the SRA toolkit binaries are in your path. 1 which fastq-dump Should produce the full path to your fastq-dump binary. If it’s not present, then we’ll need to add the directory where it is stored to your path.

Conda Tutorial

Getting started with conda Here are some reasons conda might be a useful tool for your research: Installing a second version of a system executable for testing. Software version requirements of a tool that cannot be satisfied using system installs (newer version needed). Using software that is difficult to compile from source. Using software packages that have been optimized for conda environments. Maintaining separate environments for individual research/development projects. References:

DT library tutorial

Download the Rmd file Background Purpose Show examples of the powerful javascript library DataTables with R package DT These tables are displayed in HTML and I routinely use this package in my analysis reports The tables are interactive! One can easily: Sort & search Add column filters based on the datatype Add plug-ins so one can download (as excel, csv, pdf, etc.