BioC Asia, 2019

Sydney, Australia


View the Project on GitHub Bioconductor/BiocAsia


BioC Asia 2019

5-6 December, 2019
Charles Perkins Centre, Camperdown Campus of University of Sydney, NSW, Australia

General Information

This year a large portion of the BioC Asia conference will be shared with AMSI’s BioInfoSummer.

Note that the annual ABACBS conference, this year joined with GIW, will be held the following week (9-11 of December) in Sydney.


Registration for BioC Asia is $60 for both days for students and $120 for anyone else.

Note that registration has closed.


The conference will be held at the Charles Perkins Centre:

John Hopkins Drive, The University of Sydney, Sydney, NSW 2006

Code of Conduct

Please be aware that during this event you are expected to follow the University of Sydney’s code of conduct. **In particular, the BioC Asia conference aims to provide a supportive, collegial, and harassment-free environment. **

If someone makes you or anyone else feel unsafe or unwelcome, please report it as soon as possible. Harassment and other code of conduct violations reduce the value of our event for everyone. We want you to be happy at our event. People like you make our event a better place.

You can make a report either personally or anonymously. You can make an anonymous or non-anonymous report here: It is a free-form text box that will be forwarded to conference organizers.

We can’t follow up an anonymous report with you directly, but we will fully investigate it and take whatever action is necessary to prevent a recurrence.

You can make a personal report with any of the members of the conference committee: Peter Hickey, Saskia Freytag, Dario Strbenac and Stephen Pederson.

When taking a personal report, our staff will ensure you are safe and cannot be overheard. They may involve other event staff to ensure your report is managed properly. Once safe, we’ll ask you to tell us about what happened. This can be upsetting, but we’ll handle it as respectfully as possible, and you can bring someone to support you. You won’t be asked to confront anyone and we won’t tell anyone who you are.

Our team will be happy to help you! We value your attendance.

Keynote Speakers

We are pleased to annouce three international keynote speakers:

Helena Crowell: Helena earned her undergraduate degree at the Univeristy of Heidelberg in Biochemistry. She then went on to earn her Master’s degree in Computational Biology & Bioinformatics at the ETH Zurich. She is currently a PhD candidate in Statistical Bioinformatics at the University of Zurich.

Helena focuses on developing analysis frameworks for CyTOF data and differential discovery in scRNA-seq data. She is the author of a popular Bioconductor package providing tools for preprocessing and analysis of cytometry data.

Martin Morgan: Martin earned his undergraduate and Master’s degrees in Botany at the University of Toronto. Martin’s PhD studies at the University of Chicago involved the evolutionary consequences of frequency-dependent selection, and of multilocus deleterious mutation. Martin is currently at the Roswell Park Comprehensive Cancer Center in Buffalo.

Martin leads the core team that maintains the Bioconductor project. He is the author of many Bioconductor packages and a renowned biostatistican.

Elana Fertig: Elana is an Associate Professor of Oncology at Johns Hopkins University. Prior to entering the field of computational cancer biology, Elana was a NASA research fellow in numerical weather prediction.

Elana runs a hybrid computational and experimental lab in the systems biology of cancer and therapeutic response. Her computational methods blend mathematical modeling and artificial intelligence to determine the biomarkers and molecular mechanisms of therapeutic resistance from multi-platform genomics data.

Invited Speakers

Joshua Ho, The University of Hong Kong

John Marioni, The University of Cambridge

Shila Ghazanfar, The University of Cambridge


The conference will feature selected talks (15mins), lightning talks (5mins), and software demos (5mins).

Abstract submission has closed.


There will be 9 workshops to be held on Thursday and Friday. Participants can elect to attend 3.

Abstract submission has closed.

All workshops are open to BioInfoSummer participants. For the workshops please note that:

To connect to a VM for BiocAsia 2019, please follow these instructions

If your VM doesn’t start, the following code should work:

pkgs <- c(
    "cluster", "survival", "randomForest", "missForest", "glmnet", "Rcpp", 
    "foreach", "itertools", "iterators", "Matrix", "devtools", "impute",
    "WangLab-MSSM/DreamAI/Code", "PengyiYang/PhosR", "directPA", "ClueR", 
    "Bioconductor/BiocIntro", "usethis", "roxygen2", "devtools", "goodpractice",
    "BiocCheck", "ExperimentHub", "CATALYST", "diffcyt", "sa-lee/fluentGenomics", 
    "workflowr", "ICC", "clustree", "HDCytoData"

Contents of the VM data folder can be downloaded from here

Travel Awards

There will be a number of travel awards available, with priority given to support students and early career researchers. You must submit an abstract for a talk, software demo, or workshop to be eligible for a travel award.

Travel award applications have closed.

Thursday: 5 December, 2019

Bioconductor Workshops are in Seminar Room 1.1

Provisional Timetable

8:45am - 9:00am Registration
9:00am - 9:30am Orientation and project updates
Martin Morgan
Session 1 Chair: Paul Harrison  
9:30am - 10:00am Investigating higher order interactions in single cell data with scHOT
Shila Ghazanfar - invited talk
10:00am - 10:15am Integration of multiple single-cell CyTOF datasets to untangle the heterogeneity of cancer patients’ responses to a new class of anti-cancer drugs
Marie Trussart
10:15am - 10:20am A gene orientated approach to analysis of Hi-C data from immune cells
Hannah Coughlan
10:20am - 10:25am A workshop on single-cell RNA-seq analysis
PuXue Qiao
10:25am - 10:30am Seamless visualization of complex genomic variations in GMOs and edited cell lines using gmoviz
Kathleen Zeglinski
10:30am - 11:00am Morning Tea
Session 2 Chair: Alexandra Garnham  
11:00am - 11:15am Use R/Bioconductor for Nanopore RNA-seq data analysis
Xueyi Dong
11:15am - 11:30am topconfects: rank differentially expressed genes using confidence bounds on fold change, with multiple testing adjustment
Paul Harrison
11:30am - 11:35am Network-based Classification with ClassifyR
Dario Strbenac
11:35am - 11:40am Modelling for heteroscedastic groups in RNA-seq data
Charity Law
11:40 - 11:45am Buffer time  
11:45am - 12:15pm Visualisation and analysis of circular RNAs using Ularcirc
Joshua Ho - invited speaker
12:15pm - 1:30pm Lunch  
1:30pm - 3:00pm Bioinformatics Workshop Stream A:
Pei Wang - Imputation and data quality control for proteomics data
(description, materials)
Bioinformatics Workshop Stream B:
Pengyi Yang - Computational analysis for biological discovery from (phospho)proteomic data
(description, materials)
Bioconductor Workshop Stream C:
Martin Morgan - R and Bioconductor for Genomic Analysis

(description, materials)
3:00pm - 3:30pm Afternoon Tea
3:30pm - 4:30pm Bioinformatics Workshop Stream A:
Pei Wang - Imputation and data quality control for proteomics data
(description, materials)
Bioinformatics Workshop Stream B:
Ben Crossett, David Maltby & Angela Connolly - Introduction to proteomics
(description, materials)
Bioconductor Workshop Stream C:
Peter Hickey & Saskia Freytag - Building a Bioconductor package

(description, materials)
Session 3 Chair: Dave Tang  
4:30pm - 4:45pm Gene Set Testing for Differentially Methylated Regions
Jovana Maksimovic
4:45pm - 4:50pm A tidy wrapper suite that introduces a unifying grammar for single-cell and bulk transcriptomic analyses
Stefano Mangiola
4:50pm - 4:55pm An Introduction to currently available scATAC-seq data analysing tools
Haoyu Yang
5:00pm - 6:00pm Bioinfosummer Poster Session  
6:00pm - 7:30pm Public Lecture: The bright future of applied statistics
Rafael Irizarry
7:30pm - 9:00pm Pub  

Friday: 6 December, 2019

Morning presentations are in The Hub, outside of Charles Perkins Centre main entry. Afternoon workshops in Dry Lab 1.1, Dry Lab 1.2 and Dry Lab 1.3.

Provisional Timetable

8:45am - 9:00am Registration
Session 4 Chair: Peter Hickey  
9:00am - 9:40am How to advance science using Bioconductor
Martin Morgan - keynote speaker
9:40am - 9:55am The RNAseq123 workflow package in Bioconductor
Matthew Ritchie
9:55am - 10:10am ClinSV: Detection of clinically relevant structural and copy number variation from whole genome sequencing
Andre Minoche
10:10am - 10:15am Experiences of a First-Time Package Contributor
Stephen Pederson
10:15am - 10:20am schex avoids overplotting for large single cell RNA-sequencing datasets
Saskia Freytag
10:20am - 10:25am COmapR: Genetic length calculation from crossover events
Ruqian Lyu
10:25am - 10:30am Buffer time  
10:30am - 11:00am Morning Tea
Session 5 Chair: Marie Trussart  
11:00am - 11:20pm Single cell analysis with Mass Cytometry; technology introduction and opportunities in clinical studies
Helen McGuire - invited speaker
11:20am - 12:00pm On differential discovery in high-dimensional cytometry data
Helena Crowell - keynote speaker
12:00pm - 12:30pm Ethics of precision medicine
Lisa Dive
12:30pm - 1:30pm Lunch  
1:30pm - 3:30pm Bioconductor Workshop Stream A:
Helena Crowell - Differential discovery in high-dimensional cytometry data

(description, materials)
Bioconductor Workshop Stream B:
Stuart Lee - Fluent genomics: a plyranges and tximeta case-study

(description, materials)
Bioinformatics Workshop Stream C:
Dave Tang - Reproducible bioinformatics
(description, materials)
3:30pm - 3:50pm Afternoon Tea
Session 5 Chair: Dario Strbenac  
3:50pm - 4:45pm Defining immune signatures of therapeutic response with non-negative matrix factorization of bulk and single cell data
Elana Fertig - keynote speaker
4:45pm - 5:00pm Closing Remarks  


In Case of Questions

If you have any questions regarding the conference please email Peter via

Conference Committee