LF903 - Quantitative Skills for System Biology: basic programming with R. Module for PhD/postgrads, 10x3hr session on Wednesday pm, plus 2 hour exam. Contact Sasha Ott (firstname.lastname@example.org) if you would like to join (open to others if space).
Oxford Spring School - Advanced Methods for Social Scientists https://www.politics.ox.ac.uk/spring-school/timetable.html?schoolid=517
Bioinformatics training - https://bioinfotraining.bio.cam.ac.uk/postgraduate
R User Group/Conference
Warwick R User Group: http://www2.warwick.ac.uk/fac/sci/wdsi/events/wrug/ - including resources!
Eurpoean R Users Meeting: http://2018.erum.io/
R markdown: http://rmarkdown.rstudio.com
R Documentation: http://www.rdocumentation.org/
RStudio cheatsheets (dplyr, rmarkdown, RStudio): https://www.rstudio.com/resources/cheatsheets/ - second page has cheatsheet of keyboard shortcuts (also customisable)
R for Stata users: http://www.princeton.edu/~otorres/RStata.pdf
Introduction to LaTex: https://www.sharelatex.com/learn/Learn_LaTeX_in_30_minutes
Additional material from last year’s workshop (more on LaTeX + markdown and programming to avoid copy-pasting code for similar tasks): https://www2.warwick.ac.uk/fac/sci/wdsi/events/vacationschool2017/for-participants/materials/additional/
bookdown: e-books created with R markdown, good quality and free! https://bookdown.org/
Quick-R: website with associated book containing useful how-to’s http://www.statmethods.net/
Advanced R: to learn more about R as a programming language http://adv-r.had.co.nz/
Many books/e-books in Warwick library, e.g.
- The art of R programming (Norman Matloff)
- Data Analysis and Graphics Using R (John Maindonald and John Braun)
Programming Q & A site: http://stackoverflow.com/. Use tags to refine search, e.g. “[r] [ggplot2] remove legend title”.
RStudio Community forum: https://community.rstudio.com/. A new site for discussion/help on issues particularly related to the RStudio IDE and the tidyverse set of packages (including tidyr and dplyr, see https://www.tidyverse.org/).
More on getting help on R: https://www.r-project.org/help.html
Finding out about R packages etc
R Seek: http://rseek.org/
CRAN task views: https://cran.r-project.org/web/views/ and Bioc task views: https://www.bioconductor.org/packages/release/BiocViews.html
Miscellaneous mentioned in last session
citation("pkgName") informs you how to cite a package that has been critical to your work;
citation() gives the citation to use for R itself.
Results from community poll: “How do you currently discover and learn about R packages?” (n=1099) https://app.doopoll.co/poll/FGZqTL7vpaaCgpWCM/live-results
Why sharing data and code is a good idea: https://www.nature.com/naturejobs/science/articles/10.1038/nj7461-243a
Structuring your project materials to share: https://github.com/ropensci/rrrpkg
Example compendia sharing data + R code
- Zenodo: https://zenodo.org/record/61312#.WbFTJheQxWM, https://zenodo.org/record/375944#.WbFTXxeQxWM
- Figshare: https://figshare.com/articles/R_code_and_data/5010767
- Dryad: http://datadryad.org/resource/doi:10.5061/dryad.8mj66m5c
- WRAP:http://wrap.warwick.ac.uk/90238/, http://wrap.warwick.ac.uk/75491/
Warwick researchers are encouraged to
- deposit in the repository most aligned with and most likely to be searched by colleagues in your field, with WRAP as a back-up.
- inform the WRAP team if a deposit is made elsewhere, so that a metadata record can be created to link to the deposit. The data should only be stored in one place (to avoid problems of versioning and precedence).
More advice on managing your research data: http://www2.warwick.ac.uk/services/library/staff/research/research-data/preserving-research-data