I’ve started to organize my commonly used R code into libraries, and have made them available on GitHub. Note that these are not yet well-commented and don’t have unit tests. Please open issues for any bugs you find.

The available packages are:

  • knitrtools: Some useful tools for use with knitr document generation. Of particular interest is the figr.ref function, which relies on kfigr and provides nice formatting of intra-document references.
  • fancyplots: Implementation of specific plot types, mostly for genetic/genomic data including phylogenetic trees (see radial.phylog), spatial data (see plot.genome.data), and GWAS results.
  • statTests: Implementation of various statistical tests and distributions.
  • intensities: Methods for transformation and plotting of hybridization array intensity data. Includes a single-method implementation of tQN normalization.
  • geneticsFormats: Methods for converting between different genetics formats.
  • DEUtils: Convenience methods for working with RNA-Seq differential expression R packages, including DESeq2, DEXSeq, and GO enrichment.
  • miscUtils: Some miscellaneous functions, mostly for working with IO and collection data types.
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