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?... [Read more...]

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...]

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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 ... [Read more...]

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...]

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...]

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...]

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...]

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... [Read more...]

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... [Read more...]

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...]

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... [Read more...]

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, etc. And lots of times I’ll need ... [Read more...]

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...]

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... [Read more...]

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...]

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... [Read more...]

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...]

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 with an overview of making heatmaps ... [Read more...]