Avatar

Luke Zappia

Bioinformatician (he/him)

Biography

I am a bioinformatics postdoctoral researcher in the Theis Lab at the Helmholtz Zentrum München Institute of Computational Biology and the Technische Universität München. My research focuses on the analysis of single-cell RNA sequencing data including the development and benchmarking of computational methods. I am also interested in how best to visualise data more generally.

I completed my PhD in the Oshlack Lab.

Interests

  • scRNA-seq analysis
  • Data visualisation
  • R programming

Education

  • Doctor of Philosophy (Bioinformatics), 2019

    The University of Melbourne/Murdoch Children's Research Institute

  • Master of Science (Bioinformatics), 2015

    The University of Melbourne

  • Bachelor of Science (Chemistry), 2011

    The University of Melbourne

  • Diploma in Informatics, 2011

    The University of Melbourne

Recent Posts

Exploring the SCE-verse

Analysis of packages that use the SingleCellExperiment object

Bioconductor 3.7 wrap-up

A wrap-up of the Bioconductor 3.7 release.

My AFL-Elo model

My Elo model for predicting AFL games.

Welcome to Blogdown!

My new Blogdown blog.

Joining the Dots Twitter analysis

Analysis of Twitter activity at the Joining the Dots visualisation symposium.

Projects

Phd Commits

Functions for scraping git commits from repositories associated with a PhD (or anything else) and plotting them.

R Package Development Workshop

Materials for the COMBINE Australia R package development workshop

clamour

An R package for setting up a website to display analysis of Twitter hashtags

Twitter Stats

Analysis of Twitter activity for hashtags from various events, usually academic conferences.

clustree

CRAN R package for creating clustering trees, a visualisation for looking at clustering across resolutions.

scRNA-tools

Database and website cataloguing software tools for analysing single-cell RNA sequencing data.

Splatter

Bioconductor R package for simulating scRNA-seq data.

prettytc

A Python script for pretty printing of TeXcount output

Recent & Upcoming Talks

Tools and techniques for single-cell RNA sequencing data

My PhD completion seminar

Tools, simulations and trees for scRNA-seq

Presentation at the Institute of Computational Biology where I described my PhD projects.

Using clustering trees to visualise scRNA-seq data

Selected talk at the Genome Informatics 2018 conference where I described how clustering trees can be used with scRNA-seq data.

clustree: producing clustering trees using ggraph

Presentation at the userR! 2018 conference introducing the clustree package and demonstrating how it makes use of the ggraph package.

Clustering trees for visualising scRNA-seq data

Selected talk at the Oz Single Cells 2018 conference where I presented clustering trees and the clustree package.

Recent Publications

Opportunities and challenges in long-read sequencing data analysis

Long-read technologies are overcoming early limitations in accuracy and throughput, broadening their application domains in genomics. …

Tools and techniques for single-cell RNA sequencing data

RNA sequencing of individual cells allows us to take a snapshot of the dynamic processes within a cell and explore differences between …

Nephron progenitor commitment is a stochastic process influenced by cell migration

Background

Human kidney organoids hold promise for studying development, disease modelling and drug screening. However, the utility of …