1. Crisis in reproducibility
2. An opportunity and insipration
3. Willingness to learn and share
4. Support of an open source community

• Reproducibility in cancer research is not as good as we would like
• Looked at our internal data analysis methods
• Dependent on expensive click and go software packages

[https://www.nature.com/news/1-500-scientists-lift-the-lid-on-reproducibility-1.19970]

• Proteomics data
• Submitted for publication
• Analysis not robust enough
• Set out to learn more….
• data viz I couldn't do in Excel

• A few lines of code = new data viz!

nba_heatmap <- heatmap(nba_matrix, 
                       Rowv=NA, Colv=NA, 
                       col = cm.colors(256), scale="column")

• Our data for a publication
• Alsagaby SA, et al J Proteome Res. 2014 13:5051-62 doi: 10.1021/pr5002803

My first cluster dendrogram

# make the cluster dendrogram object using the hclust() and dist() functions
hc <- hclust(dist(rbind(P1, P2, P3, P4, P5, P6, P7, P8, P9, P10, P11, P12)))  

# plot the cluster dendrogram 
plot(hc, xlab = "Patient Samples")

• My professional society - the Biochemical Society.
• Suggested a training day in R
• Then, I was organising it and delivering it
• Created a blog: R for Biochemists
• Delivered a training day - June 2015
• Further training in Cardiff, Germany and Namibia

• R for Biochemists Blog

• R User Group
• Making packages - talk on 2nd of November
• twitter: @brennanpcardiff #rstats

• A package is a collection of R functions
• Created and shared with the community
• Packages are being developed regularly
• Hosted on github, CRAN, Bioconductor

• Bringing together webscraping and data visualisation
• Our bodies are made up of cells
• These cells depend on molecules called proteins
• Built a package to generate visualistions of these proteins

• Testing functions
• Package coverage
• Documentation

Keratin - an important skin and hair protein

## [1] "Download has worked"

• TIME and PATIENCE
• Inspiration
• Reasons to stay committed
• Open Source Learning & Teaching

• Thanks for the invitation
• Cardiff University pays my salary
• Biochemical Society for support & advertising for the R for Biochemists Training day
• Biochemcial Society - online training
• CaRdiff R-Users Group - Stef Locke and Dave Parr
• This presentation made in Rmarkdown using R-Studio