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/.
A post on creating a Gantt chart using R; these are good for showing a project timeline in grant applications. The code is adapted from an answer on Stack Overflow. You will need the ggplot2 and reshape2 packages; install them if you haven't already.
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.
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
I finally found the reason behind the sporadic 500 internal server errors on my blog. It was caused by the iThemes Security plugin, which had modified the .htaccess file in a manner that was causing the errors. I have disabled the plugin and the site seems to be running fine now. I've also added HTTPS on my domain, so you can now access my blog on https://davetang.org/muse/. Enjoy!
How many pathogenic ClinVar variants are in intergenic regions? I'll define genomic regions as per this old post. To get started, download the latest ClinVar variants:
wget -c ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar_20170104.vcf.gz # index tabix -p vcf clinvar_20170104.vcf.gz # how many variants? zcat clinvar_20170104.vcf.gz | grep -v "^#" | wc -l 232624