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.

Bioinformatics

basejump
Base functions for bioinformatics and R package development.
bioverbs
S4 generic functions for bioinformatics.
brio
Biological R input/output.
freerange
Generate and manipulate genomic ranges.
syntactic
Make syntactically valid names out of character vectors.
transformer
Coercion methods for Bioconductor data classes.
acidplots
Functions for plotting genomic data.

Functional genomics

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

Shell configuration

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

Package development

goalie
Assertive check functions for defensive R programming.
bb8
Trusty sidekick for R package development.
acidroxygen
Shared documentation files for R packages.
acidtest
Reference data for unit testing.