Second Asia-Pacific Bioconductor Meeting

Venue: QUT, Brisbane, Australia

Date: Friday 4th November 2016

Overview. The Bioconductor project has undergone significant growth over the past 15 years, with over 1,200 packages for high-throughput genomic analysis included in the latest release. Many popular software tools from the project are developed by researchers from the Asia-Pacific region. To enhance collaboration and provide an avenue for networking, the Second Bioconductor Asia meeting will be held following the ABACBS 2016 conference ( This one-day event aims to bring together researchers with an interest in the Bioconductor project to provide a forum for exchanging ideas and future plans for software development. We welcome attendance from users and package developers (both current and prospective). The meeting will consist of a number of longer talks selected from abstracts and short ‘lightning’ presentations to maximize the opportunities for participants to highlight their work. A developer workshop to build skills on a topic of shared interest will also be held.

Key dates. Email proposals for longer talks / lightning talks to (Title and abstract of up to 300 words) by Friday 7th October 2016.

Location. All presentations will take place at QUT Gardens Point in Q228.


9:00am-9:55am Project Updates (Prof Martin Morgan)
9:55am-10:30am Lightning talks

Soroor Hediyeh Zadeh 'OPPAR: Outlier Profile and Pathway Analysis'
Ted Wong 'Anaquin - quantitative controls with spike-ins'
Jovana Maksimovic 'A Bioconductor Workflow for Methylation Array Analysis'
Jason Ross 'The Development of the R/Bioconductor build of Harman’
Dario Strbenac 'ClassifyR: Classification Convenience in R’
Goknur Giner ‘Introducing R-LadiesAU’
10:30am-11:00am Morning Tea
11:00am-12:30pm Research talks (4 x 20 minutes each)
Session Chair : Jovana Maksimovic

Belinda Phipson ‘Analysing DNA methylation array data with missMethyl: going beyond differential methylation’
Tim Peters ‘DMRcate, a complete DMR-calling Bioconductor package’
Andy Chen ‘Analyzing Bisulfite sequencing methylation data using edgeR’
Hien To ‘rnaCleanR: A tool for quantifying and removing DNA contamination from strand-specific RNA-seq’
12:30pm-1:20pm Lunch
3:00pm-3:30pm Research talks (5 x 20 minutes each)
Session Chair : Stephen Pederson

Charity Law ‘Glimma, getting greater graphics for your genes’
Davis McCarthy ‘scater: pre-processing, quality control, normalisation and visualisation for single-cell RNA-seq data’
Goknur Giner ‘FRY: A Fast Approximation to ROAST Gene Set Test with Mean Aggregated Set Statistics’
Monther Alhamdoosh ‘Combining multiple tools outperforms individual methods in gene set enrichment analyses’
Cynthia Liu ‘KRLMM: a SNP genotyping method for both common and low-frequency variants in any organism’
3:00pm-3:30pm Afternoon Tea
3:30pm-4:10pm Keynote: Keynote: Gordon Smyth ‘A short history of limma and edgeR’
4:10pm-4:30pm Discussion and closing remarks

Travel scholarships.

A number of scholarships ($500 AUD each) are available for students and Bioconductor package developers to help with the cost of travel to attend the meeting. To apply, please submit a brief statement (200 words or less) describing your interest in the meeting. If you are a package developer or maintainer please tell us the package(s) you work on. The due date for applications is Friday 7th October 2016. Please send applications to and include SCHOLARSHIP in the subject line.

Registration IS CLOSED.



Dr Matt Ritchie, Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia

Dr Jovana Maksimovic, Murdoch Childrens Research Institute, Melbourne, Australia

Mr Stephen Pederson, Bioinformatics Centre, The University of Adelaide, Adelaide, Australia

The organisers are grateful to AGTA (, ABACBS ( and CSL Limited ( for their financial support of this meeting.