Blog Archives

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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Shiny Developer Conference 2016 Recap

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 labeli...

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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 sid...

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

December 4, 2015
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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 samp...

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Annotables: R data package for annotating/converting Gene IDs

November 13, 2015
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I work with gene lists on a nearly daily basis. Lists of genes near ChIP-seq peaks, lists of genes closest to a GWAS hit, lists of differentially expressed genes or transcripts from an RNA-seq experiment, lists of genes involved in certain pathways, et...

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Software from CSHL Genome Informatics 2015

November 2, 2015
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Software from CSHL Genome Informatics 2015

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...

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Compiling RMarkdown from a Helper R Script

August 6, 2015
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Compiling RMarkdown from a Helper R Script

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 di...

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R: single plot with two different y-axes

April 21, 2015
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R: single plot with two different y-axes

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 th...

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R User Group Recap: Heatmaps and Using the caret Package

April 10, 2015
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R User Group Recap: Heatmaps and Using the caret Package

At our most recent R user group meeting we were delighted to have presentations from Mark Lawson and Steve Hoang, both bioinformaticians at Hemoshear. All of the code used in both demos is in our Meetup’s GitHub repo.Making heatmaps in RSteve started...

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