steinbaugh.com

Computational and scientific resources provided by Michael Steinbaugh.

Software

basejump
Base functions for bioinformatics and R package development.
rnaiscreen
Automated scoring for a C. elegans genome-wide RNAi screen.
seqcloud
High-performance computing scripts for next-generation sequencing.
worminfo
C. elegans gene annotations and RNAi clone mappings.

Articles

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.

HBC-affiliated resources

Software

bcbioRnaseq
Quality control and differential expression for bcbio-nextgen RNA-seq experiments.
bcbioSinglecell
Utility functions for analysis of bcbio-nextgen single-cell RNA-seq data.
bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis.

Training

Interactive courses offered at HMS covering a number of current bioinformatics-related topics:

  1. Introduction to the Unix command line.
  2. Working in a high-performance computing (HPC) environment.
  3. Programming with R.
  4. Standard bulk RNA-seq analysis.
  5. Single-cell RNA-seq analysis (in development).

Source materials are available at the hbctraining organization on GitHub.