Bioinformatics resources provided by Michael Steinbaugh.

Software

basejump
Base functions for bioinformatics and R package development.
bb8
Trusty sidekick for R package development.
bcbioBase
Base functions and generics for bcbio R packages.
bcbioRNASeq
R package for bcbio RNA-seq analysis.
bcbioSingleCell
R package for bcbio single-cell RNA-seq analysis.
brightworm
Automated scoring for a C. elegans genome-wide RNAi screen.
DESeqAnalysis
Toolkit for performing differential expression with DESeq2.
goalie
Assertive check functions for defensive R programming.
koopa
Shell bootloader for bioinformatics.
pointillism
R package for for single-cell RNA-seq clustering analysis.
wormbase
C. elegans genome annotations from WormBase.

Posts

git quick reference
. Reference commands for the git version-control system.
tmux quick reference
. Reference commands for the tmux terminal multiplexer.
Install macOS
. How to make that Mac feel new again.
Install bcbio
. bcbio is a python toolkit providing current best practice pipelines for next-generation sequencing data analysis.
Install R on an HPC cluster using bioconda
. Maintain a consistent R environment across HPC environments with conda.
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 a Raspberry Pi device
. How to get a Pi up and running in less than 15 minutes.
Interactive R on an HPC cluster
. How to run R in an interactive session.
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.
C. elegans resources
. Links to worm tools around the web.
Programming style rules
. Clean code, happy life.
Install Ubuntu
. Ubuntu Linux is a great programming environment but it’s more difficult to initially set up than macOS or Windows.