Blog Archives

Staying Current in Bioinformatics & Genomics: 2017 Edition

February 1, 2017
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A while back I wrote this post about how I stay current in bioinformatics & genomics. That was nearly five years ago. A lot has changed since then. A few links are dead. Some of the blogs or Twitter accounts I mentioned have shifted focus or haven?...

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RStudio Conference 2017 Recap

January 14, 2017
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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...

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Covcalc: Shiny App for Calculating Coverage Depth or Read Counts for Sequencing Experiments

June 1, 2016
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Covcalc: Shiny App for Calculating Coverage Depth or Read Counts for Sequencing Experiments

How many reads do I need? What's my sequencing depth? These are common questions I get all the time. Calculating how much sequence data you need to hit a target depth of coverage, or the inverse, what's the coverage depth given a set amount of sequenci...

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Covcalc: Shiny App for Calculating Coverage Depth or Read Counts for Sequencing Experiments

June 1, 2016
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Covcalc: Shiny App for Calculating Coverage Depth or Read Counts for Sequencing Experiments

How many reads do I need? What's my sequencing depth? These are common questions I get all the time. Calculating how much sequence data you need to hit a target depth of coverage, or the inverse, what's the coverage depth given a set amount of sequenci...

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Shiny Developer Conference 2016 Recap

February 5, 2016
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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 University. I’ve built a handful of apps, and have taught...

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Shiny Developer Conference 2016 Recap

February 5, 2016
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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...

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Repel overlapping text labels in ggplot2

January 8, 2016
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Repel overlapping text labels in ggplot2

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 gene name. But if you want to annotate lots...

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Repel overlapping text labels in ggplot2

January 8, 2016
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Repel overlapping text labels in ggplot2

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
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GRUPO: Shiny App For Benchmarking Pubmed Publication Output

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 sid...

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GRUPO: Shiny App For Benchmarking Pubmed Publication Output

December 14, 2015
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GRUPO: Shiny App For Benchmarking Pubmed Publication Output

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 code behind the app is written in R, and leverages the NCBI...

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