Software I've (co-)authored

This page provides links to R packages I have (co-)authored. The most recent versions of most packages are on, and Most packages are also on CRAN.

Analysing single-cell omics data

  • anndata for R: Annotated Data in R, CRAN
  • dynbenchmark: Pipeline for benchmarking trajectory inference methods
  • dyndimred: Applying dimensionality reduction methods, CRAN
  • dyneval: Evaluating trajectory inference methods
  • dynfeature: Calculating feature importance scores from trajectories
  • dyngen: Simulating single-cell data using gene regulatory networks, CRAN
  • dynguidelines: User guidelines for trajectory inference
  • dynmethods: A collection of wrappers for trajectory inference methods
  • dyno: A pipeline for inferring, visualising and interpreting trajectories
  • dynparam: Creating meta-information for parameters, CRAN
  • dynplot: A simple visualisation library for trajectories
  • dynplot2: A fully customisable visualisation library for trajectories
  • dyntoy: Generating simple toy data of cellular differentiation
  • dynutils: Common functionality for the dynverse packages, CRAN
  • dynwrap: A common format for trajectories, CRAN
  • SCORPIUS: Inferring developmental chronologies from single-cell omics, CRAN


  • diffusionMap: Implements diffusion map method of data parameterization CRAN
  • GillespieSSA: Gillespie’s Stochastic Simulation Algorithm (SSA), CRAN
  • GillespieSSA2: Gillespie’s Stochastic Simulation Algorithm for Impatient People, CRAN
  • gng: Growing Neural Gas implemented in Rcpp
  • incgraph: Incremental graphlet counting for network optimisation, CRAN
  • lmds: Landmark Multi-Dimensional Scaling, CRAN
  • princurve: Fits a principal curve in arbitrary dimension, CRAN
  • proxyC: Computes proximity in large sparse matrices, CRAN

Software development


I also help maintain or extend other packages on Github, CRAN or Bioconductor on which I often depend.

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