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 github.com/rcannood or github.com/dynverse. Most packages are also on CRAN.

Analysing single-cell omics data

  • 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
  • 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

Algorithms

  • 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

  • babelwhale: Interacting with Docker and Singularity containers, CRAN
  • qsub: Running commands remotely on gridengine clusters, CRAN

Contributions

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