Articles by Stephen Turner

RStudio Conference 2017 Recap

January 14, 2017 | Stephen Turner

The first ever RStudio conference was held January 11-14, 2017 in Orlando, FL. For anyone else like me who spends hours each working day staring into an RStudio session, the conference was truly excellent. The speaker lineup was diverse and covered lot... [Read more...]

Shiny Developer Conference 2016 Recap

February 5, 2016 | Stephen Turner

This is a guest post from VP Nagraj, a data scientist embedded within UVA’s Health Sciences Library, who runs our Data Analysis Support Hub (DASH) service.Last weekend I was fortunate enough to be able to participate in the first ever Shiny Developer Conference hosted by RStudio at Stanford ... [Read more...]

Shiny Developer Conference 2016 Recap

February 5, 2016 | Stephen Turner

This is a guest post from VP Nagraj, a data scientist embedded within UVA’s Health Sciences Library, who runs our Data Analysis Support Hub (DASH) service.Last weekend I was fortunate enough to be able to participate in the first ever Shiny Develope... [Read more...]

Repel overlapping text labels in ggplot2

January 8, 2016 | Stephen Turner

A while back I showed you how to make volcano plots in base R for visualizing gene expression results. This is just one of many genome-scale plots where you might want to show all individual results but highlight or call out important results by labeling them, for example, with a ... [Read more...]

Repel overlapping text labels in ggplot2

January 8, 2016 | Stephen Turner

A while back I showed you how to make volcano plots in base R for visualizing gene expression results. This is just one of many genome-scale plots where you might want to show all individual results but highlight or call out important results by labeli... [Read more...]

GRUPO: Shiny App For Benchmarking Pubmed Publication Output

December 14, 2015 | Stephen Turner

This is a guest post from VP Nagraj, a data scientist embedded within UVA’s Health Sciences Library, who runs our Data Analysis Support Hub (DASH) service.The WhatGRUPO (Gauging Research University Publication Output) is a Shiny app that provides side-by-side benchmarking of American research university publication activity.The HowThe ... [Read more...]

Tutorial: RNA-seq differential expression & pathway analysis with Sailfish, DESeq2, GAGE, and Pathview

December 4, 2015 | Stephen Turner

BackgroundThis tutorial shows an example of RNA-seq data analysis with DESeq2, followed by KEGG pathway analysis using GAGE. Using data from GSE37704, with processed data available on Figshare DOI: 10.6084/m9.figshare.1601975. This dataset has six samples from GSE37704, where expression was quantified by either: (A) mapping to to GRCh38 using ... [Read more...]

Software from CSHL Genome Informatics 2015

November 2, 2015 | Stephen Turner

I just returned from the Genome Informatics meeting at Cold Spring Harbor. This was, hands down, the best scientific conference I've been to in years. The quality of the talks and posters was excellent, and it was great meeting in person many of the scientists and developers whose tools and ... [Read more...]

Compiling RMarkdown from a Helper R Script

August 6, 2015 | Stephen Turner

The problemI was looking for a way to compile an RMarkdown document and have the filename of the resulting PDF or HTML document contain the name of the input data that it processed. That is, if I compiled the analysis.Rmd file, where in that file it did some analysis ... [Read more...]

R: single plot with two different y-axes

April 21, 2015 | Stephen Turner

I forgot where I originally found the code to do this, but I recently had to dig it out again to remind myself how to draw two different y axes on the same plot to show the values of two different features of the data. This is somewhat distinct from ... [Read more...]
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