Bioinformatics and functional genomics tools by Michael Steinbaugh.
Source code for all projects is available on GitHub.
- Shell bootloader for bioinformatics.
- Dockerfile recipes for our Docker Hub images.
- Configuration files shared between machines.
- Base functions for bioinformatics and R package development.
- Pipette biological data in and out of R.
- Functions for plotting genomic data.
- Toolkit for performing differential expression with DESeq2.
- Parameterized fast gene set enrichment analysis.
Single-cell RNA sequencing
- Toolkit for 10X Genomics single-cell RNA-seq data.
- R package for for single-cell RNA-seq clustering analysis.
These R packages for bcbio were developed at the Harvard Chan Bioinformatics Core. The software is still actively developed and maintained by Acid Genomics.
- R package for bcbio RNA-seq analysis.
- R package for bcbio single-cell RNA-seq analysis.
- Base functions and generics for bcbio R packages.
- EggNOG database annotations.
- PANTHER database annotations.
- C. elegans genome annotations from WormBase.
R package development
- Assertive check functions for defensive R programming.
- Make syntactically valid names out of character vectors.
- Trusty sidekick for R package development.
- Low-level base functions imported by Acid Genomics packages.
- S4 generics for Acid Genomics R packages.
- Shared documentation files for R packages.
- Reference data for unit testing.