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.
|slingshot||Trajectory inference methods for modeling continuous, branching processes. Designed for differentiation processes in scRNA-seq.|
|tradeSeq||Spline-based (zero-inflated) negative binomial models for continuous-time expression data and clustering of temporal expression profiles.|
|scry||Analysis methods for high-dimensional, small-count data.|
|Dune||Consensus clustering by optimal cluster merging for improved replicability in single-cell RNA-Seq cell type discovery.|
|glmpca||Implements a generalized version of principal components analysis (GLM-PCA) for dimension reduction of non-normally distributed count data.|