PGP public key
Fingerprint B829 F851 00B7 9CB7 6897 DCA7 A881 5DA8 5150 5ABF
Bioinformatics software
Topconfects: R package. Top differential expression by confident effect size. A more intuitive way to use "TREAT".
Varistran: R package. Variance stabilizing transformation for RNA-Seq data. This is a useful pre-processing step prior to visualization, and also makes clustering and statistical analysis more straightforward. Includes a shiny app for assessing RNA-seq data quality with heatmap and biplot.
Tail-Tools: Analysis pipeline for PAT-Seq data.
Nesoni: Disorganized pile of tools for processing bacterial high-throughput sequencing data.
Plasmodium Autocount and Semiautocount: Cell counting on blood smears.
Writing
Publications on Google Scholar.
PhD thesis (2005) on image texture synthesis. I also have several publications relating to my PhD work on texture.
Introduction to R, version 2 (2018) (version 1 here) Workshop material introducing R.
Programming and tidy data analysis in R (2019) (based on an ealier workshop R more (2016)). Workshop to go from beginner to intermediate R usage, which I have developed and presented with other members of the Monash Bioinformatics Platform and the Monash Data Fluency initiative.
Linear models in R (2018) Workshop material introducing linear models in R. Linear models are a very broadly useful statistical tool, and also necessary background knowledge for using Bioconductor packages such as limma.
Dance of the CIs, a Javascript app version of the "Dance of the CIs" from the "New Statistics". Illustrates the meaning of confidence intervals, standard error, standard deviation, and prediction intervals.