Acid Genomics

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

EggNOG
EggNOG database annotations.
PANTHER
PANTHER database annotations.
wormbase
C. elegans genome annotations from WormBase.

Package development

basejump
Base functions for bioinformatics and R package development.
goalie
Assertive check functions for defensive R programming.
bb8
Trusty sidekick for R package development.

Shell configuration

koopa
Shell bootloader for bioinformatics.
dotfiles
Configuration files shared between machines.