Publications by Stephen Turner
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 of the scientists and developers whose tools and software I use on a daily basis. To get a sense of w...
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Annotables: R data package for annotating/converting Gene IDs
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 to convert these gene IDs from one identifier to another. There...
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Annotables: R data package for annotating/converting Gene IDs
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 to convert these gene IDs from one identifier to another. There...
3819 sym R (4027 sym/11 pcs) 4 img 5 tbl
Tutorial: RNA-seq differential expression & pathway analysis with Sailfish, DESeq2, GAGE, and Pathview
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 STA...
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Tutorial: RNA-seq differential expression & pathway analysis with Sailfish, DESeq2, GAGE, and Pathview
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 STA...
5338 sym R (18414 sym/10 pcs) 10 img
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 behi...
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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 behi...
6305 sym R (1739 sym/4 pcs) 2 img
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 of points, the annotati...
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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 of points, the annotati...
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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 Developer Conference hosted by RStudio at Stanford University. I’ve built a handful of apps, and have t...
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