Articles by Stephen Turner

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...]

R + ggplot2 Graph Catalog

February 3, 2015 | Stephen Turner

Joanna Zhao’s and Jenny Bryan’s R graph catalog is meant to be a complement to the physical book, Creating More Effective Graphs, but it’s a really nice gallery in its own right. The catalog shows a series of different data visualizations, all made with R and ggplot2. ... [Read more...]

Importing Illumina BeadArray data into R

December 8, 2014 | Stephen Turner

A colleague needed some help getting Illumina BeadArray gene expression data loaded into R for data analysis with limma. Hopefully whoever ran your arrays can export the data as text files formatted as described in the code below. If so, you can import... [Read more...]

RNA-seq Data Analysis Course Materials

November 20, 2014 | Stephen Turner

Last week I ran a one-day workshop on RNA-seq data analysis in the UVA Health Sciences Library. I set up an AWS public EC2 image with all the necessary software installed. Participants logged into AWS, launched the image, and we kicked off the morning ... [Read more...]
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