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2 min read Bioconductor, R

Today marks the release of Bioconductor 3.7 (official announcement). Congratulations to the hundreds of developers who have collectively developed more than 1500 software packages, not to mention the annotation, experiment data, and workflow packages. A huge thank you to the core team for the incredible work they do, especially around release time! Much of my recent development work on Bioconductor has been leveraging and extending the DelayedArray framework developed by Hervé Pagès (Bioconductor Core Team).

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2 min read R

Over the Australian summer, I flew home from Baltimore to attend the wedding of two of my dearest friends, Kirsty and Kelly. I had the added excitement of helping officiate their ceremony and could not have been more thrilled. There’s was to be the first legal same-sex marriage in Tasmania, the southernmost state of Australia. Needless to say, it was a bloody incredible day, as recorded in several media articles, including The Advocate, PEDESTRIAN.

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6 min read Bioconductor, R, conference

A couple of weeks back I was in Boston for BioC2017, the annual Bioconductor meeting. This is my favourite conference because I get to hear from and meet the awesome community that develop and use R/Bioconductor packages to enable research in high-throughput biology. The agenda and slides for the 3 days are available from https://www.bioconductor.org/help/course-materials/2017/BioC2017/. I’m drawing on these notes that I scrawled during Developer Day, the first day of the meeting.

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1 min read

Earlier this year this equation was doing the rounds of the geek community. When plotted it supposedly drew the Batman symbol. Simple, no? See here for a thorough discussion of how all the pieces fit together. It would seem that you have to work pretty hard for Batman to appear in your graphs. But today I stumbled across Batman in real scientific paper. Observe… The plot comes from Supplementary Figure 11 of Li, Y.

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5 min read seminar

I attended a talk by Dr Stephen Turner, the founder and Chief Technology Officer of Pacific Biosciences, promoting PacBio’s SMRT (Single Molecule Real Time) sequencing platform. While I’d heard of the “next-next-generation” of sequencing technologies at least 18 months ago, this was the first time I’d paid much attention to them. What sets the “next-next-gen” from the “next-gen” platforms (why won’t this terminology die already!) is that rather than sequencing a cluster (Illumina) or a bead (SOLiD) of amplified and identical molecules we sequence a single molecule.

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Projects

DNA methylation

Research from my PhD and much of my postdoc

R

Some of the things I’ve done with R

Recent & Upcoming Talks

More Talks

Data Organisation: Making Your Research Life Easier
Feb 8, 2019 3:30 PM
Data Organisation workshop at ACU
Slides
Getting help and helping others (including future you)
Nov 30, 2018 11:00 AM
BioCAsia 2018
Slides Project
Genome-wide analysis of DNA methylation in samples from the Genotype-Tissue Expression (GTEx) project
Nov 5, 2018 2:10 PM
AGTA 2018
PDF Project
Lessons from switching to on-disk storage using DelayedArray containers
Jul 25, 2018 9:40 AM
BioC 2018
Project
DelayedArray: A tibble for arrays
Jul 13, 2018 10:30 AM
useR! 2018
PDF Project

Selected Publications

bioRxiv, 2017
Project bioRxiv

JOSS, 2016
Project JOSS (Open Access)

Proc. Natl. Acad. Sci. U.S.A, 2015
PubMed

Recent Publications

More Publications

. A Novel Apparatus to Measure Knee Flexor Strength During Various Hamstring Exercises: A Reliability and Retrospective Injury Study. J Orthop Sports Phys Ther., 2018.

PubMed

. Enhancing GTEx by Bridging the Gaps Between Genotype, Gene Expression, and Disease. Nat Genet., 2017.

Project PubMed

. Neuronal Brain Region-Specific DNA Methylation and Chromatin Accessibility Are Associated with Neuropsychiatric Disease Heritability. bioRxiv, 2017.

Project bioRxiv

. The Victorian Collaborative Autism Study: A Family and Community Study of the Genetics of Autism Spectrum Disorder. J Intellect Disabil Res, 2016.

Abstract

. Representation and Manipulation of Genomic Tuples in R. JOSS, 2016.

Project JOSS (Open Access)

Contact

  • peter.hickey@gmail.com
  • Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Vic, 3052, Australia

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