Please, see the schedule and the recordings of all sessions on the Hopin platform

Wednesday, August 2, 2023

Time (ET) Session Presenting author(s) Title/Event YouTube
08:00 Registration Registration/Breakfast
08:30 Keynote Vince Carey Introduction
09:00 Keynote JJ Allaire Keynote: Reproducible Manuscripts with Quarto
10:00 Short talks track Afrooz Razi
Pedro Baldoni
Sonali Arora
Daianna Gonzalez-Padilla


10:00 Short talks track Brian Schilder
Qian Liu
Jayaram Kancherla
Stefano Mangiola


10:00 Short talks track Kinnary Shah
Nicholas J Eagles
Yi Wang
Sowmya Parthiban

Spatial transcriptomics

11:00 Short talks track Nicholas Cheng
Ryan C Thompson
Lauren Marie Harmon
Peter Yizhou Huang

Epigenetics and multi-omics track

11:00 Package demo Mercedeh Movassagh mbQTL: An R/Bioconductor Package for Microbial Quantitative Trait Loci (QTL) Estimation
11:00 Short talks track Xiuwen Zheng
Meghana Kshirsagar
Jae Min Park
Zachary DeBruine


12:00 Lunch break Lunch break
13:00 Keynote Sam Lent Keynote: Weighing the benefits and risks of making 'de-identifiable' genomics data public
14:00 Package demo Louise A. Huuki-Myers Analyzing Spatially-Resolved Transcriptomics Data from Visium using spatialLIBD
14:00 Workshop Arpan Neupane Reproducible and programmatic analysis of flow cytometry experiments with the cytoverse**
14:00 Workshop Jiefei Wang High-Performance Computing in R for Genomic Research**
15:00 Package demo Jiaji George Chen Giotto Suite: A multi-scale and technology-agnostic spatial omics analysis framework
16:00 Break-Networking Break/Networking
16:30 Package demo Ellis Patrick Statial: A Bioconductor package for identifying spatially-related changes in cell state
16:30 Package demo Stevie M Pederson extraChIPs: Detection and Visualisation of Differential ChIP-Seq Signal
16:30 Package demo Qian Liu Use R to Create and Execute Reproducible CWL Workflows for Genomic Research
Workshop/demo levels: * - beginner, recommended for starting with Bioconductor; ** - intermediate; *** - advanced.

Thursday, August 3, 2023

Time (ET) Session Presenting author(s) Title/Event YouTube
08:00 Breakfast Breakfast
08:30 Keynote Beth Cimini Keynote: Making the most of your microscopy with high-content analysis
09:30 Short talks track Sara Stankiewicz
Jacob Krol
Natasha Gurevich

Cancer, Evolution

09:30 Short talks track Jared T Brown
Harkirat Kaur Sohi
Peiying Cai
Shiheng Huang

Spatial transcriptomics

09:30 Package demo Jacques Serizay Orchestrating Hi-C analysis with Bioconductor
10:30 Birds of a Feather Maria Doyle Bioconductor Carpentries global teaching program
10:30 Birds of a Feather J Wokaty Cloud Methods
10:30 Package demo Zuguang Gu rGREAT: an R/Bioconductor Package for Functional Enrichment on Genomic Regions
11:30 Awards Awards
12:00 Lunch break Lunch break
13:00 Keynote Jeff Moffitt Keynote: Imaging the Transcriptome: Creating Tissue Atlases with MERFISH
14:00 Workshop Vincent James Carey Bridges from python to Bioconductor: applications in genetics and single-cell genomics**
14:00 Workshop Daianna Gonzalez-Padilla A Bioconductor-style differential expression analysis powered by SPEAQeasy*
14:00 Package demo Chloe Anya Mirzayi Epidemiology for Bioinformaticians
15:00 Package demo Marcel Ramos Multi-omic Integration and Analysis of cBioPortal and TCGA data with MultiAssayExperiment
16:00 Break-Networking Break/Networking
16:30 Birds of a Feather Bioconductor and the Latin American Bioinformatics Landscape: Challenges and Opportunities
16:30 Short talks track Noor Pratap Singh
Molly Martorella
Matt McCall
Sean Maden
Jean-Philippe Fortin

16:30 Short talks track Outreachy team
Atuhurira Kirabo Kakopo
Beryl Kanali
Jen Wokaty

Outreachy Birds of a Feather

17:30 Posters Poster session
Workshop/demo levels: * - beginner, recommended for starting with Bioconductor; ** - intermediate; *** - advanced.

Friday, August 4, 2023

Time (ET) Session Presenting author(s) Title/Event YouTube
08:30 Breakfast Breakfast
09:00 Keynote Heng Li Keynote: Genome assembly in the telomere-to-telomere era
10:00 Short talks track Mengbo Li
Simone Tiberi
Samuel David Gamboa-Tuz
Leo M Lahti

Microbiome, Proteomics

10:00 Short talks track Ahmad Al Ajami
Phillip Nicol
Joshua Campbell
Jill Lundell


10:00 Package demo Stefano Mangiola Tidy genomic and transcriptomic single-cell analyses
11:00 Short talks track Alexandru Mahmoud
Lucas Schiffer
Sehyun Oh
Zuguang Gu


11:00 Package demo Hedia Tnani Differential Expression Analysis using Limma and qsvaR
11:00 Package demo Michael P Lynch demuxSNP: supervised demultiplexing of scRNAseq data using cell hashing and SNPs
11:30 Meet the team Meet the Core
11:30 Meet the team Meet the Community Advisory Board (CAB)
11:30 Meet the team Meet the Technical Advisory Board (TAB)
12:00 Lunch break Lunch break
13:00 Keynote Nancy Zhang Keynote: Spatial transcriptomics data analysis: Cancer subclone detection and niche-differential expression analysis
14:00 Workshop Lambda Moses Voyager: Exploratory spatial data analysis from geospatial to spatial -omics**
14:00 Package demo Jianhong Ou A shiny application for single cell RNA-seq visualization
14:00 Workshop Eric Scott Davis Mariner: Explore the Hi-Cs**
15:00 Talk track Lightning Talks
16:00 Talk track Lightning Talks
16:00 Package demo Izabela Mamede Conceição Isoformic: Isoform level biological interpretation from transcriptomic data
16:00 Package demo Yingxin Lin Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2
Workshop/demo levels: * - beginner, recommended for starting with Bioconductor; ** - intermediate; *** - advanced.