csdaw/candidaev: Final accepted manuscript

candidaev

This repository contains the research compendium for our paper:

> Dawson, C. S., Garcia-Ceron, D., Rajapaksha, H., Faou, P., Anderson, M. A., Bleackley, M. R. (2020) Protein markers for Candida albicans EVs include claudin-like Sur7 family proteins. Journal of Extracellular Vesicles, x(x): 1750810. DOI: 10.1080/20013078.2020.1750810

The compendium includes all the data, code, and text associated with the publication. The raw MS data has been deposited in the ProteomeXchange Consortium database via the PRIDE partner repository with the data set identifiers PXD014367, PXD014388, and PXD014389. 

All vignettes, `candidaev_manuscript.Rmd`, `candidaev_supplement.Rmd`, and the supplementary data `.R` scripts have all been tested and knit/run successfully. These reproduce the results presented in the paper.

Session Info

Here is sessionInfo() output from compiling candidaev_manuscript.Rmd. This document was compiled was on a MacBook Pro running MacOS 10.15.3 and pandoc v2.9.2.

R version 3.6.2 (2019­12­12)

Platform: x86_64­apple­darwin15.6.0 (64­bit)

locale: en_AU.UTF­8||en_AU.UTF­8||en_AU.UTF­8||C||en_AU.UTF­8||en_AU.UTF­8

attached base packages: stats, graphics, grDevices, utils, datasets, methods and base

other attached packages: kableExtra(v.1.1.0.9000), ggpubr(v.0.2.5), magrittr(v.1.5), gg­plot2(v.3.3.0), dplyr(v.0.8.5), limma(v.3.42.2), tidyNano(v.0.1.2.2) and candidaev(v.2.2.1)

loaded via a namespace (and not attached): Biobase(v.2.46.0), httr(v.1.4.1), tidyr(v.1.0.2), viridisLite(v.0.3.0), shiny(v.1.4.0.2), assertthat(v.0.2.1), pander(v.0.6.3), yaml(v.2.2.1), ggre­pel(v.0.8.2), pillar(v.1.4.3), backports(v.1.1.6), lattice(v.0.20­40), glue(v.1.4.0), digest(v.0.6.25), RColorBrewer(v.1.1­2), promises(v.1.1.0), ggsignif(v.0.6.0), rvest(v.0.3.5), colorspace(v.1.4­1), cowplot(v.1.0.0), htmltools(v.0.4.0), httpuv(v.1.5.2), pkgconfig(v.2.0.3), GetoptLong(v.0.1.8), broom(v.0.5.5), bookdown(v.0.18), purrr(v.0.3.3), xtable(v.1.8­4), scales(v.1.1.0), webshot(v.0.5.2), VennDiagram(v.1.6.20), later(v.1.0.0), tibble(v.3.0.0), generics(v.0.0.2), farver(v.2.0.3), ellipsis(v.0.3.0), withr(v.2.1.2), BiocGenerics(v.0.32.0), cli(v.2.0.2), crayon(v.1.3.4), mime(v.0.9), evaluate(v.0.14), fansi(v.0.4.1), nlme(v.3.1­145), xml2(v.1.2.5), tools(v.3.6.2), hms(v.0.5.3), GlobalOptions(v.0.1.1), formatR(v.1.7), lifecycle(v.0.2.0), ComplexHeatmap(v.2.2.0), stringr(v.1.4.0), munsell(v.0.5.0), cluster(v.2.1.0), lambda.r(v.1.2.4), pcaMethods(v.1.78.0), compiler(v.3.6.2), rlang(v.0.4.5), futile.logger(v.1.4.3), grid(v.3.6.2), rstudioapi(v.0.11), rjson(v.0.2.20), circlize(v.0.4.8), labeling(v.0.3), rmarkdown(v.2.1), gtable(v.0.3.0), R6(v.2.4.1), gridExtra(v.2.3), knitr(v.1.28), fastmap(v.1.0.1), clue(v.0.3­57), futile.options(v.1.0.1), shape(v.1.4.4), readr(v.1.3.1), stringi(v.1.4.6), parallel(v.3.6.2), Rcpp(v.1.0.4.6), vctrs(v.0.2.4), png(v.0.1­7), tidyselect(v.1.0.0) and xfun(v.0.12)