Bioinformatics resources provided by Michael Steinbaugh.

Software

R

RNA sequencing

bcbioRNASeq
R package for bcbio RNA-seq analysis.
DESeqAnalysis
Toolkit for performing differential expression with DESeq2.
pfgsea
Parameterized fast gene set enrichment analysis.

Single-cell RNA sequencing

bcbioSingleCell
R package for bcbio single-cell RNA-seq analysis.
Chromium
Toolkit for 10X Genomics single-cell RNA-seq data.
pointillism
R package for for single-cell RNA-seq clustering analysis.

Functional genomics

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

Package development

basejump
Base functions for bioinformatics and R package development.
bioverbs
S4 generic functions for bioinformatics.
brio
Biological R input/output.
syntactic
Make syntactically valid names out of character vectors.
transformer
Additional S3 and S4 coercion methods for easy interconversion between Bioconductor and tidyverse data classes.
bb8
Trusty sidekick for R package development.
goalie
Assertive check functions for defensive R programming.

Shell

dotfiles
My dot files shared between machines.
koopa
Shell bootloader for bioinformatics.

Posts

Install conda
. Quick installation guide for conda, along with tips for managing environments.
Detect the Illumina sequencer model
. Extract the Illumina sequencer instrument information from a FASTQ file.
Cache R package library on Travis CI
. How to cache an R/Bioconductor package with multiple dependencies.
Vim quick reference
. Reference commands for the vim text editor.
Tmux quick reference
. Reference commands for the tmux terminal multiplexer.
Install a Raspberry Pi device
. How to get a Pi up and running in less than 15 minutes.
Git quick reference
. Reference commands for the git version-control system.
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.
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.
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.