Acid Genomics

Bioinformatics and functional genomics tools by Michael Steinbaugh.

Source code for all projects is available on GitHub.


RNA sequencing

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

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

DepMapAnalysis
Cancer Dependency Map (DepMap) analysis toolkit.
cBioPortalAnalysis
Toolkit for performing queries on cBioPortal.
Cellosaurus
Cellosaurus identifier mapping toolkit.
EggNOG
EggNOG database annotations.
PANTHER
PANTHER database annotations.
WormBase
C. elegans genome annotations from WormBase.

Bioinformatics

basejump
Base functions for bioinformatics and R package development.
pipette
Pipette biological data in and out of R.
AcidPlots
Functions for plotting genomic data.

R infrastructure

goalie
Assertive check functions for defensive R programming.
syntactic
Make syntactically valid names out of character vectors.
AcidBase
Low-level base functions imported by Acid Genomics packages.
AcidGenerics
S4 generics for Acid Genomics R packages.
AcidRoxygen
Shared documentation files for R packages.
AcidTest
Reference data for unit testing.
bcbioBase
Base functions and generics for bcbio R packages.
bb8
Trusty sidekick for R package development.

Shell configuration

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

Continuous integration

docker
Dockerfile recipes for our Docker Hub images.
Rcheck
Scripts for Dockerized continuous integration tests.