Acid Genomics

Bioinformatics and functional genomics tools by Michael Steinbaugh.

Source code for all projects is available on GitHub.

RNA sequencing

DESeqAnalysis
Toolkit for performing differential expression with DESeq2.
pfgsea
Parameterized fast gene set enrichment analysis.

Single-cell RNA sequencing

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

bcbio-nextgen

These R packages for bcbio-nextgen were developed at the Harvard Chan Bioinformatics Core. The software is still actively developed and maintained by Acid Genomics.

bcbioRNASeq
R package for bcbio RNA-seq analysis.
bcbioSingleCell
R package for bcbio single-cell RNA-seq analysis.
bcbioBase
Base functions and generics for bcbio R packages.

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.
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.

R package development

goalie
Assertive check functions for defensive R programming.
syntactic
Make syntactically valid names out of character vectors.
bb8
Trusty sidekick for R package development.
bioverbs
S4 generic functions for bioinformatics.
acidbase
Low-level base functions imported by Acid Genomics packages.
acidroxygen
Shared documentation files for R packages.
acidtest
Reference data for unit testing.