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

• Developer Day: Wednesday, July 25.
• Day 1: Thursday July 26.
• Day 2: Friday July 27.

Developer Day: Wednesday July 25

See the Developer Day schedule.

Day 1: Thursday July 26

Logistics:

• Start your course AMI
• Join the bioc-community slack

8:00 - 8:45 – Registration and breakfast, VC second floor foyer

8:45 - 9:00 – Welcoming remarks – slides (Martin Morgan)

VC 213 Chapel

9:00 - 9:30 – Michael Hoffman University of Toronto.

Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome – VC 213 Chapel

9:30 - 10:00 – Elana Fertig John Hopkins University.

Enter the Matrix: Interpreting omics through matrix factorization – VC 213 Chapel

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 – VC 213 Chapel

11:00 - 12:00 – Contributed talks – VC 213 Chapel

• 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 – VC Foyer and Alumni Hall

• Organizing and coordinating R / Bioconductor meetups – VC 211

1:00 - 2:45 – Workshop Session 1a

• Martin Morgan*. Bioconductor for Everyone – VC 212
• Ludwig Geistlinger* and Levi Waldron. Functional enrichment analysis of high-throughput omics data – VC 215

1:45 - 2:45 – Workshops Session 1b

• Zhaleh Safikhani*, Petr Smirnov, Benjamin Haibe-Kains. Biomarker discovery from large pharmacogenomics datasets – VC 206

2:45 - 3:15 – Break

3:15 - 5:00 – Workshops Session 2a

• MacDonald J, Shepherd L. Introduction to Bioconductor annotation resources – VC 206
• Love MI. RNA-seq data analysis with DESeq2 – VC 215

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 – SET UP your laptop for this workshop by arriving at 3:30. For the workshop download and install cytoscape 3.6.1 and workshop files – VC 212

5:30 - 7:30 – Contributed posters – VC Foyer and Alumni Hall

Day 2: Friday July 27

8:00 - 8:30 – Breakfast, VC Second floor foyer

8:30 - 9:00 – Tim Hughes, University of Toronto.

Binding motifs for DNA and RNA binding proteins – VC 213 Chapel

9:00 - 9:30 – Benjamin Haibe-Kains, Princesss Margaret Cancer

Center, Toronto.

Cancer Biomarker Discovery: Building a Bridge Between Preclinical and Clinical Research – VC 213 Chapel

9:30 - 10:00 – Contributed talks – VC 213 Chapel

• 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 – VC 213 Chapel

11:00 - 12:00 – Contributed talks – VC 213 Chapel

• 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 – VC Foyer and Alumni Hall

1:00 - 2:45 – Workshops Session 3a

• Michael Lawrence*, Martin Morgan. Solving common bioinformatic challenges using GenomicRanges – VC 215
• Ramos M, Geistlinger L, Waldron L*. Workflow for Multi-omics Analysis with MultiAssayExperiment – VC 212

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 – VC 206

2:45 - 3:15 – Break

3:15 - 5:00 – Workshops Session 4a

• Das D*, Street K*, Risso D*. Analysis of single-cell RNA-seq data: Dimensionality reduction, clustering, and lineage inference – VC 215
• Nicholas Cooley*, Erik Wright. Working with Genomic Data in R with the DECIPHER package – VC 212
• Levi Waldron, Benjamin Haibe-Kains, Sean Davis. Public Data Resources and Bioconductor – VC 211

4:00 - 5:00 – Workshops Session 4b

• Lee S*, Lawrence M. Fluent genomic data analysis with plyranges – VC 206

5:30 - 7:30 – Contributed posters – VC Foyer and Alumni Hall