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.reffunction, 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.