Software

I have contributed to multiple software packages for the analysis of genomic data. I am a proponent of open-source software and all packages are freely available.

Bioconductor

slingshotTrajectory inference methods for modeling continuous, branching processes. Designed for differentiation processes in scRNA-seq.
tradeSeqSpline-based (zero-inflated) negative binomial models for continuous-time expression data and clustering of temporal expression profiles.
scryAnalysis methods for high-dimensional, small-count data.
DuneConsensus clustering by optimal cluster merging for improved replicability in single-cell RNA-Seq cell type discovery.

CRAN

glmpcaImplements a generalized version of principal components analysis (GLM-PCA) for dimension reduction of non-normally distributed count data.