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Novartis Genentech
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Ontario Institute for Cancer Research
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University of Toronto

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BioC 2018: Where Software and Biology Connect

When: July 25 (Developer Day) 26 and 27, 2018
Where: Victoria University, University of Toronto, Toronto, Canada
Twitter: #bioc2018

Schedule

Confirmed Speakers for July 26-27

Developer Day: Wednesday July 25

See the Developer Day schedule.

Day 1: Thursday July 26

8:00 - 8:45 – Registration
8:45 - 9:00 – Welcoming remarks (Martin Morgan)
9:00 - 9:30 – Michael Hoffman University of Toronto.
Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome.
9:30 - 10:00 – Elana Fertig John Hopkins University.
Enter the Matrix: Interpreting omics through matrix factorization.
10:00 - 10:30 – Break
10:30 - 11:00 Brenda Andrews University of Toronto.
Analysis of high content microscopy data generated through automated yeast genetics.
11:00 - 12:00 – Contributed talks
  • Innes BT* and Bader GD. scClustViz - Single-cell RNAseq Cluster Assessment and Interactive Visualisation.
  • Righelli D*, Koberstein J, Gomes B, Zhang N, Angelini C, Peixoto L, Risso D. Differential Enriched Scan 2 (DEScan2): a fast pipeline for broad peak analysis.
  • Adithya M, Bhargava A, Wright E*. Improving the accuracy of taxonomic classification for identifying taxa in microbiome samples.
  • Zhun Miao*, Ke Deng, Xiaowo Wang, Xuegong Zhang. DEsingle for detecting three types of differential expression in single-cell RNA-seq data.
  • Ludwig Geistlinger*, Gergely Csaba, Mara Santarelli, Lucas Schiffer, Marcel Ramos, Ralf Zimmer, and Levi Waldron. Towards a gold standard for benchmarking gene set enrichment analysis.
12:00 - 1:00 – Lunch / Birds-of-a-feather
1:00 - 2:45 – Workshop Session 1
  • Martin Morgan*. Bioconductor for Everyone.
  • Ludwig Geistlinger* and Levi Waldron. Functional enrichment analysis of high-throughput omics data.
1:45 - 2:45 – Workshops Session 1b
  • Zhaleh Safikhani*, Petr Smirnov, Benjamin Haibe-Kains. Biomarker discovery from large pharmacogenomics datasets.
2:45 - 3:15 – Break
3:15 - 5:00 – Workshops Session 2
  • MacDonald J, Shepherd L. Introduction to Bioconductor annotation resources
  • Love MI. RNA-seq data analysis with DESeq2
4:00 - 5:00 – Workshops Session 2b
  • Coetzee SG* and Hazelett DJ. Variant Functional Annotation using StatePaintR, FunciVar and MotifBreakR.
  • Isserlin R*,Innes B, Bader GD. Cytoscape Automation in R using Rcy3.
5:30 - 7:30 – Contributed posters

Day 2: Friday July 27

8:30 - 9:00 – Tim Hughes, University of Toronto.
Binding motifs for DNA and RNA binding proteins.
9:00 - 9:30 – Benjamin Haibe-Kains, Princesss Margaret Cancer
Center, Toronto.
Cancer Biomarker Discovery: Building a Bridge Between Preclinical and Clinical Research.
9:30 - 10:00 – Contributed talks
  • Lee S*, Cook D, Lawrence M. plyranges: a fluent interface to Bioconductor’s Ranges infrastructure.
  • Love MI*, Hickey P, Soneson, C, and Patro R. Automatic metadata propagation for RNA-seq.
10:00 - 10:30 – Break
10:30 - 11:00 – Charlotte Soneson, University of Zurich, Switzerland.
A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs.
11:00 - 12:00 – Contributed talks
  • Albert Y Zhang, Shian Su, Matthew E Ritchie, and Charity W Law*. Unpacking signal from RNA-seq intron reads using Rsubread and limma packages.
  • Steinbaugh MJ*, Kirchner RD, Ho Sui S. bcbioSingleCell: R package for bcbio single-cell analysis.
  • Abbas Rizvi*, Ezgi Karaesmen*, Leah Preus, Michael Sovic, Junke Wang, Lara Sucheston-Campbell. gwasurvivr: an R package to perform survival association testing on imputed genetic data.
  • Nima Hejazi*, Alan Hubbard, Mark van der Laan. Data-Adaptive Estimation and Inference for Differential Methylation Analysis.
  • Rachael V Phillips*, Alan Hubbard. Data Adaptive Evaluation of Preprocessing Methods using Ensemble Machine Learning.
12:00 - 1:00 – Lunch / Birds-of-a-feather
1:00 - 2:45 – Workshops Session 3
  • Michael Lawrence*, Martin Morgan. Solving common bioinformatic challenges using GenomicRanges.
  • Ramos M, Geistlinger L, Waldron L*. Workflow for Multi-omics Analysis with MultiAssayExperiment.
1:45 - 2:45 – Workshops Session 3b
  • Charity Law* , Monther Alhamdoosh, Shian Su, Gordon Smyth and Matthew Ritchie. RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR.
2:45 - 3:15 – Break
3:15 - 5:00 – Workshops Session 4
  • Das D*, Street K*, Risso D*. Analysis of single-cell RNA-seq data: Dimensionality reduction, clustering, and lineage inference.
  • Nicholas Cooley*, Erik Wright. Working with Genomic Data in R with the DECIPHER package.
  • Levi Waldron, Benjamin Haibe-Kains, Sean Davis. Public Data Resources and Bioconductor.
4:00 - 5:00 – Workshops Session 4b
  • Lee S*, Lawrence M. Fluent genomic data analysis with plyranges
5:30 - 7:30 – Contributed posters