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, github.com/dynverse and github.com/data-intuitive. 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
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
- randpy: versioned R and Python Docker containers, Docker Hub
Contributions
I also help maintain or extend other packages on Github, CRAN or Bioconductor on which I often depend.
- Algorithmic optimisations: slingshot
- Extend functionality: ggrepel, ParamHelpers, ranger, rlang
- Fix bugs: devtools, monocle, proxyC, rticles, shadowtext
- Maintain packages: diffusionMap, princurve, GillespieSSA
- Documentation: devtools, mlr, remotes, tidyverse, ŋraphsim, MaterialNet
- Continuous integration: Rdimtools, slingshot, monocle, splatter, SingleCellOpenProblems