Research

A guide to elegant tiled heatmaps in R [2019]

A step-by-step guide to data preparation and plotting of simple, neat and elegant heatmaps in R using base graphics and ggplot2.

Beautiful circos plots in R

Circos plots are popular for displaying huge amounts of data in a relatively small visual space. This is especially relevant for genomic data. This post explores creating Circos-style genomic data plots in R using R package circlize.

Fast LD computation from VCF files using Tomahawk

Fast LD computation from a VCF file using **vcftools**, **bcftools** and **tomahawk**. This avoids the use of PLINK or conversion to PLINK formats.

Customising ggplot2

Customising a ggplot2 plot using the theme function. In this post, we are going to explore how to adjust various ggplot plot elements. What can be adjusted, what they are called and how they can be adjusted.

Scraping Instagram and choosing hashtags

Scraping Instagram for basic public data using R to help us pick "optimal" hastags.

Running ImageJ on a Linux cluster

A quick tutorial on running ImageJ on a Linux cluster.

Multiple Statistical Testing

In the advent of big data such as genomics, running numerous statistical tests is unavoidable. But long comes strange statistical problems. This post investigates issues with multiple statistical testing and its solutions along with simulated data.

Humanity has never lived in better times

It is easy to be disillusioned and pessimistic about the world we live in. Bad news seems to be followed by worse news. But humanity has come a long way from the disease-ridden, impoverished, war-torn lives of our fore-fathers. Here we look at a few data-driven graphs to convince ourselves of the progress we have made over time in various aspects of life. Slow progress never makes headlines.

Read counts of RNA-Seq Spike-ins using STAR and QoRTs

A short tutorial on quantifying spike-ins used in an RNA-Seq experiment.

Which file compression to use on Linux?

This is a quick comparison of some of the data compression and decompression formats on Linux. The idea is to compare compression/decompression time and compression size difference using seven compression formats on five different file types.