BioC 2019: Where Software and Biology Connect

When: June 24 - 27, 2019
What: Developer Day, Main Conference, Symposium
Where: NYU and Rockefeller University, New York City, USA
Slack: Bioconductor Team (#bioc2019 channel)
Twitter: #bioc2019

Day 1: Tuesday June 25

8:00 - 8:45 – Registration and breakfast – Abby Lounge

8:45 - 9:00 – Welcoming remarks – Martin Morgan – Caspary Auditorium

9:00 - 9:30 – Jeffrey Leek – Caspary Auditorium

9:30 - 10:00 – Elli Papaemmanuil – Caspary Auditorium

10:00 - 10:30 – Simina Boca – Caspary Auditorium

10:30 - 11:00 – Break – CRC Lower Level

11:00 - 12:00 – Contributed talks Session 1a - Single-cell theme – Caspary Auditorium

• Robert A. Amezquita – Orchestrating Single-Cell Analysis with Bioconductor
• Helena L. Crowell – Analysis of multi-sample multi-group scRNA-seq data
• Shian Su – CellBench: A Framework for Evaluating Single Cell Analysis Pipelines
• Stephanie Hicks – mbkmeans: fast clustering for single cell data using mini-batch k-means
• Deepayan Sarkar – Gene Set Enrichment Analysis with Multi-omics Data

11:00 - 12:00 – Contributed talks Session 1b - Statistical methods – Carson Auditorium

• Nima Hejazi – Generalized Variance Moderation for Locally Efficient Estimation in High-Dimensional Biology
• John Lawson – Coordinate Covariation Analysis (COCOA): Understanding Interindividual Variation in Data with Genomic Coordinates
• Ingo Ruczinski – Detection of rare disease variants in extended pedigrees using RVS
• Svetlana Vinogradova – ASER: eliminating transcriptome-wide batch effects results in higher precision in allele-specific expression measurements
• Katharina Imkeller – Improving accuracy of phenotype detection in whole-genome CRISPR screens

12:00 - 1:00 – Lunch / Birds-of-a-feather, sponsored by F1000 Research – Weiss South Room

1:00 - 1:50 – Workshop Session 2a

• The Basics: Bioconductor for Everyone – Martin Morgan and Lori Shepherd – RRB 110
• SingleCell: Effectively using the DelayedArray framework to support the analysis of large data sets – Pete Hickey – Carson Auditorium
• RNAseq & Omics: Workflow for Multi-omics Analysis with MultiAssayExperiment and curatedTCGAData – Marcel Ramos, Ludwig Geistlinger, and Levi Waldron – Weiss 301
• Genomics & Enrichment Analysis: Tools for region-based genomic analysis – Nathan Sheffield – Weiss 305

2:00 - 2:50 – Workshop Session 2b

• The Basics: Bioconductor for Everyone – Martin Morgan and Lori Shepherd – RRB 110
• SingleCell: Effectively using the DelayedArray framework to support the analysis of large data sets – Pete Hickey – Carson Auditorium
• RNAseq & Omics: Workflow for Multi-omics Analysis with MultiAssayExperiment and curatedTCGAData – Marcel Ramos, Ludwig Geistlinger, and Levi Waldron – Weiss 301
• Genomics & Enrichment Analysis: Tools for region-based genomic analysis – Nathan Sheffield – Weiss 305

2:50 - 3:10 – Break – Weiss South Room

3:10 - 4:00 – Workshop Session 3a

• The Basics: Fluent genomic workflows with plyranges – Stuart Lee – Weiss 305
• SingleCell: Orchestrating Single-Cell Analysis with Bioconductor: Overview and Workflows – Robert A. Amezquita, Vince J. Carey, Lindsay N. Carpp, Ludwig Geistlinger, Aaron T. L.Lun, et al. – Carson Auditorium
• RNAseq & Omics: Bioinformatics tools for integrating and understanding molecular changes associated with with Immune Response, Stemness and Oncogenic processes – Antonio Colaprico, Gabriel Odom, Lily Wang, & Xi Chen – Weiss 301
• Genomics & Enrichment Analysis: Copy number variation analysis with Bioconductor – Ludwig Geistlinger, Marcel Ramos, Seyhun Oh, and Levi Waldron – RRB 110

4:10 - 5:00 – Workshop Session 3b

• The Basics: A plyranges and tximeta case study: differential expression and accessibility – Michael Love – Weiss 305
• SingleCell: Analysis of large single-cell RNA-seq datasets in R/Bioconductor – Davide Risso and Stephanie Hicks – Carson Auditorium
• RNAseq & Omics: Working with open-source Human Microbiome Project Data: Efficient Data Access and Analysis Workflow – Levi Walrdon, Ni Zhao, Mikhail Dozmorov, Ekaterina Smirnova – Weiss 301
• Genomics & Enrichment Analysis: ATAC-seq data quality control using the ATACseqQC package – Haibo Liu, Jianghong Ou, and Julie Lihua Zhu – RRB 110

5:30 - 7:30 – Contributed posters

• Group-A posters – Weiss Lobby
• Lightning talks (concurrent with posters) – Weiss 301
• Poster dimensions up to 58 inches wide x 40 inches tall. Individual poster allocations will be affixed to poster boards.