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
A quick and short post on parallel distance calculation in R using the mclapply() function from the parallel package. I'll use data from the Biobase and datamicroarray packages to illustrate.