Richard Cotton

In scholarly publications, multiple graphical elements such as plots or raster images are traditionally combined into a single compound figure using panels arranged in a grid. Package multipanelfigure is a GPL-3 licensed R package that eases assembly of such compound figures, allowing for straightforward integration of R specific plots using base graphics, lattice and ggplot2 plots, as well as grid grobs in general. Also provided are facilities to incorporate R external graphical output stored… Show more

In scholarly publications, multiple graphical elements such as plots or raster images are traditionally combined into a single compound figure using panels arranged in a grid. Package multipanelfigure is a GPL-3 licensed R package that eases assembly of such compound figures, allowing for straightforward integration of R specific plots using base graphics, lattice and ggplot2 plots, as well as grid grobs in general. Also provided are facilities to incorporate R external graphical output stored as SVG, PNG, JPEG, or TIFF formatted files. Show less

“flippant” allows for quick, reproducible data analysis of scramblase activity assays and provides a platform for review, dissemination and extension of the strategies it employs.

Genome-wide association studies (GWAS) with intermediate phenotypes, like changes in metabolite and protein levels, provide functional evidence to map disease associations and translate them into clinical applications. However, although hundreds of genetic variants have been associated with complex disorders, the underlying molecular pathways often remain elusive. Associations with intermediate traits are key in establishing functional links between GWAS-identified risk-variants and disease end… Show more

Genome-wide association studies (GWAS) with intermediate phenotypes, like changes in metabolite and protein levels, provide functional evidence to map disease associations and translate them into clinical applications. However, although hundreds of genetic variants have been associated with complex disorders, the underlying molecular pathways often remain elusive. Associations with intermediate traits are key in establishing functional links between GWAS-identified risk-variants and disease end points. Here we describe a GWAS using a highly multiplexed aptamer-based affinity proteomics platform. We quantify 539 associations between protein levels and gene variants (pQTLs) in a German cohort and replicate over half of them in an Arab and Asian cohort. Fifty-five of the replicated pQTLs are located in trans. Our associations overlap with 57 genetic risk loci for 42 unique disease end points. We integrate this information into a genome-proteome network and provide an interactive web-tool for interrogations. Our results provide a basis for novel approaches to pharmaceutical and diagnostic applications. Show less

Paper accompanying my R package for importing and working with SomaLogic ADAT files.

A mixed proteomics and transcripomics analysis of mesenchymal stem cells.

Comparing urinary thallium levels in people working with thallium vs. background levels.

Paper to accompany PopGen, a web app that genereates virtual human populations, for use in PBPK modelling.

An introduction to the R programming language, covering the full data analysis workflow and a wide variety of R packages. 400 pages of statistical goodness.

I wrote the chapter entitled "Blood, sweat and urine". It combines ten pages of insight into data management in a scientific organisation with wee jokes.

I did the stats analysis on this. The fun part was running mixed effects models on censored data.

I examined the distributions of creatinine levels in men and women. Mostly remarkable for the big (in biological monitoring terms) dataset.

How to do sensitivity analysis for PBPK models. In which I invent the Lowry plot, for visualising the sensitivity of different parameters in a system of ODEs.

A simple analysis of variation between people in the uptake/elimination curves for a few chemicals.

Stats analysis of blood samples from people who work with lead. Features some MCMC modelling with WinBUGS and a load of number crunching with R.

Stats analysis of swimming data from tagged plaice, based upon my masters degree thesis.