steinbaugh.com

Bioinformatics resources provided by Michael Steinbaugh.

Software

basejump
Base functions for bioinformatics and R package development.
seqcloud
High-performance computing shell bootloader.
bb8
Trusty sidekick for R package development.

Harvard Chan Bioinformatics Core

bcbioBase
Base functions and generics for bcbio R packages.
bcbioRNASeq
Quality control and differential expression for bcbio RNA-seq experiments.
bcbioSingleCell
Import and analyze bcbio single-cell RNA-seq data.

C. elegans genetics

wormbase
C. elegans genome annotations from WormBase.
rnaiscreen
Automated scoring for a C. elegans genome-wide RNAi screen.

Articles

Install R on an HPC cluster using bioconda

. Maintain a consistent R environment across HPC environments with conda.

Interactive R on an HPC cluster

. How to run R in an interactive session.

Clean install macOS

. How to make that Mac feel new again.

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.

Clean install Ubuntu

. Ubuntu Linux is a great programming environment but it’s more difficult to initially set up than macOS or Windows.

Clean install a Raspberry Pi device

. How to get a Pi up and running in less than 15 minutes.