Web traffic to date


I'm going to include my blog as a form of community engagement in my fellowship application. The only objective way I can measure its impact is by the number of views. Luckily the WordPress API makes it easy to download all my web traffic and I have made this data available online. I wrote this post in case one of the assessors decided to check whether I was just making up numbers.

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Intersect in R

A colleague asked me this question: "I'm trying to find a way to find genes that overlap between three datasets. I have used intersect for two dataframes but can't seem to find a solution for three dataframes on google. Do you know any snazzy way of doing that?" I thought using the venn() function from the gplots package is a pretty snazzy solution, so that's what I recommended.

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A single exome

In the age of 50,000+ and 60,000+ whole exome catalogues, it's hard to find processed data for a single exome. At least I had trouble trying to find a single VCF file for a single exome from one individual. After searching for a while, I gave up and decided to generate one myself. This post is on how I generated a single VCF file, which I have hosted on my web server.

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Basic Shiny app to fetch variant information

I created a basic Shiny app that uses the myvariant package to fetch variant information from MyVariant.info. The variants need to be represented in the format recommended by the Human Genome Variation Society. Once you have your variant of interest in the correct format, just hit "Get variant info!" and the annotations will appear on the right. You can find the app hosted at: https://davetang.shinyapps.io/get_variant_info/.

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ExAC allele frequency of pathogenic ClinVar variants

A continuation of the post on the genomic location of pathogenic ClinVar variants. For this post I will use vcfanno to annotate the ClinVar variants with the ExAC VCF file.

To get started, download the ExAC VCF file.

# 4.1G file
wget -c ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/ExAC.r0.3.1.sites.vep.vcf.gz
wget -c ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/ExAC.r0.3.1.sites.vep.vcf.gz.tbi

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