Bioinformatics resources provided by Michael Steinbaugh.

R packages have migrated to Acid Genomics.


Vim cheat sheet
. Reference commands for the vim text editor.
Spacemacs cheat sheet
. Reference commands for the spacemacs text editor.
Raspberry Pi cheat sheet
. Additional recommended software configuration for Raspberry Pi.
Install Raspberry Pi OS
. Install the official 32-bit Raspberry Pi OS.
Install Ubuntu on Raspberry Pi
. Install the 64-bit ARM variant of Ubuntu on a Raspberry Pi.
Tmux cheat sheet
. Reference commands for the tmux terminal multiplexer.
Git cheat sheet
. Reference commands for the git version-control system.
Docker cheat sheet
. Reference commands for Docker.
AWS ECR cheat sheet
. Reference commands for creating and pushing repositories on Amazon Web Services (AWS) Elastic Container Repository (ECR) service.
GnuPG cheat sheet
. Reference commands for gpg.
bcbio-nextgen Homo sapiens reference genome
. Details on the assembly sources used for the hg38 genome build.
Ubuntu apt repositories
. Information on the default Ubuntu repositories for apt.
Docker login using pass credential store
. More secure method for working with DockerHub on Linux.
macOS Mojave fix for Rcpp compilation headers
. C++ headers are currently messed up inside R on Mojave by default.
Shell strict mode
. Make the shell stricter by default using set built-in.
POSIX shell cheat sheet
. Reference syntax and commands for POSIX shell scripting.
Detect the Illumina sequencer model
. Extract the Illumina sequencer instrument information from a FASTQ file.
Manage Ruby on macOS using rbenv
. Use a combination of Homebrew and rbenv to manage Ruby on macOS.
NCBI genomes
. Referece information regarding public NCBI genome assemblies.
Install Ubuntu
. Ubuntu Linux is a great programming environment but it’s more difficult to initially set up than macOS or Windows.
Install macOS
. How to make that Mac feel new again.
Visual Studio Code cheat sheet
. Reference commands for Microsoft’s cross-platform code editor based on Electron.
Install conda
. Quick installation guide for conda, along with tips for managing environments.
Cache R package library on Travis CI
. How to cache an R/Bioconductor package with multiple dependencies.
Install bcbio-nextgen
. bcbio is a python toolkit providing current best practice pipelines for next-generation sequencing data analysis.
Make a private fork of a public git repository
. GitHub currently only allows the creation of public forks. However, it is possible to sync code between a public repository and a private mirror.
Install RDAVIDWebService
. An R Package for retrieving data from DAVID into R objects using Web Services API.
Automounts on macOS with NFS
. The best method to automatically connect your Mac to network storage.
Programming style rules
. Clean code, happy life.
C. elegans resources
. Links to worm tools around the web.