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.
brio
Biological R input/output.
freerange
Generate and manipulate genomic ranges.
transformer
Coercion methods for Bioconductor data classes.
bcbioBase
Base functions and generics for bcbio R packages.
acidplots
Functions for plotting genomic data.
bioverbs
S4 generic functions for bioinformatics.

Data science

goalie
Assertive check functions for defensive R programming.
syntactic
Make syntactically valid names out of character vectors.

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

acidbase
Low-level base functions imported by Acid Genomics packages.
acidroxygen
Shared documentation files for R packages.
acidtest
Reference data for unit testing.
bb8
Trusty sidekick for R package development.