Conference programme

Monday 9 December

9:00 - 9:15	Registration
9:15 - 9:30	Welcome and introductions
9:30 - 10:00	Invited talk 1: Martin Morgan - The Bioconductor Project: Updates and Directions
10:00 - 10:30	Invited talk 2: Andrea Rau - Individualized multi-omic pathway deviation scores using multiple factor analysis
10:30 - 11:00	Break + poster session
11:00 - 12:00	Flashlight session 1 (7 x 8 minutes)
12:00 - 12:30	Invited talk 3: Vince Carey - Software ecosystem concepts for federated genomic analysis
12:30 - 13:30	Lunch + poster session
13:30 - 14:30	Flashlight session 2 (7 x 8 minutes)
14:30 - 15:00	Invited talk 4: Levi Waldron - Multi’omic analysis of subtype evolution and heterogeneity in high-grade serous ovarian carcinoma
15:00 - 15:30	Invited talk 5: Lieven Clement - The pitfalls of summarisation and imputation on label free mass spectrometry based proteomics
15:30 - 16:00	Coffee break + poster session
16:00 - 16:30	Invited talk 6: Christine Choirat - Enabling Practical Reproducibility With the RENKU Platform
16:30 - 17:02	Flashlight session 3 (4 x 8 minutes)
17:02 - 17:15	Presentation of group activities and wrap-up.

Evening:

18:30 - 21:30

Dinner at the Hof ter Musschen (located at walking distance from the conference venue)

The conference dinner is sponsored by GSK.

Tuesday 10 December

9:00 - 10:00	Flashlight session 4 (7 x 8 minutes)
10:00 - 10:30	Invited talk 7: Davide Risso - Efficient and scalable clustering of single-cell RNA-seq data using Bioconductor
10:30 - 11:00	Break + poster session
11:00 - 12:30	Group activities
12:30 - 13:30	Lunch + poster session
13:30 - 14:00	Group activities presentations
14:00 - 14:30	Invited talk 8: Ewa Szczurek - Linear effects models of signaling pathways from combinatorial perturbation data
14:30 - 15:00	Invited talk 9: Elisabetta Mereu - Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects
15:00 - 15:30	Invited talk 10: Andreas Moor - Spatially resolved transcriptomics in mammalian tissues
15:30 - 16:00	Wrap-up and closing of conference
16:00 - 17:00	Preparation of user/developer sessions

Wednesday 11 December (optional)

9:00 - 10:30	User/developer sessions
10:30 - 11:00	Break
11:00 - 12:30	User/developer sessions (cont.)
12:30 - 13:30	Lunch
13:30 - 15:00	User/developer sessions (cont.)
15:00 - 16:00	Sessions feedback and wrap-up

Flashlight talks

Session 1

Chair: Charlotte Soneson

Witold Wolski - fgczgseaora: unifying methods on gene set enrichment
Federico Marini - GeneTonic: combining components of transcriptome analyses for efficient exploration
Ozan Cinar - poolr: An extensive set of methods for gene-based testing
Nathalie Pochet - AMARETTO for network biomedicine: linking diseases, drivers and drugs via multi-omics, clinical, imaging and perturbation data fusion
Theo Killian - Exploiting the Depmap cancer dependency data using the depmap R package
Mike Smith - Benchmarking compression filters for HDF5 backed matrices
Anne Bras - flowCore - lossless compression

Session 2

Chair: Laurent Gatto

Katarzyna Gorczak - Transcriptomics data visualization
Ruizhu Huang - Visualizing TreeSummarizedExperiment objects and tree climbing with treeclimbR
Michela Pasetto - transcriptomicsTemplates: a template for the analysis of transcriptomics data
Axelle Loriot - Genome-wide approach to identify new transcripts induced by DNA hypomethylation in tumors
Sara Fonseca Costa - Expression calls from RNA-seq using BgeeCall R package
Katharina Hembach - exondiscovery: prediction of unannotated exons from splice-junction RNA-seq reads
Robert Castelo - GenomicScores: latest developments and future challenges

Session 3

Chair: Elisabetta Mereu

Johannes Rainer - Flexible infrastructure for mass spectrometry data
Christian Panse - Direct access to mass spectrometry data in R
Oliver Crook - Uncertainty quantification for dynamic spatial proteomics experiments
Nils Kurzawa - Robust statistical inference of small molecule-protein interactions from 2D thermal proteome profiles reveals off-targets of epigenetic drugs

Session 4

Chair: Andrea Rau

Dario Righelli - Epigenomic enrichment analysis using Bioconductor
Dania Machlab - monaLisa: MOtif aNAlysis with Lisa
Stephany Orjuela - DAMEfinder: A method to screen for changes in allele-specific methylation
Simone Tiberi - BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertainty
Almut Luetge - Explore batch effects and data integration with CellMixS
Jeroen Gilis - Scalable differential transcript usage analysis for single-cell applications
Pierre-Luc Germain - A framework for pipeline benchmarking and its application to scRNAseq clustering

Posters

Chong Tang: msdata2: Lable-Free Proteomics data for Benchmarking
Christophe Vanderaa: scpdata: a data package for single-cell proteomics
Gibb Sebastian: Spectra: a flexible infrastructure for mass spectrometry data
Teun van den Brand: GENOVA: Explore the Hi-Cs
Tore Bleckwehl: Single cell methods for regulatory elements
Mireia Ramos-Rodríguez: UMI4Cats: an R package for analyzing UMI-4C contact data
Liesbeth François: Insights into biological mechanisms of an in vitro epilepsy model by leveraging gene coexpression modules
Aliaksandra Kakoichankava: Deconvolution of transcriptomic data shows biologically and clinically relevant signals in pancreatic tumors
Tobias Kockmann & Christian Panse: Direct access to mass spectrometry data in R - the rawR package
Laurent Gatto: The R for Mass Spectrometry Initiative
Katarzyna Górczak: Transcriptomics data visualization
Pierre Luc Germain: A framework for pipeline benchmarking and its application to scRNAseq clustering
Michela Pasetto: transcriptomicsTemplates: a templates for the analysis of transcriptomics data
Sara Fonseca Costa: Expression calls from RNA-Seq data using BgeeCall R package
Nathalie Pochet: AMARETTO for network biomedicine: linking diseases, drivers and drugs via multi-omics, clinical, imaging and perturbation data fusion
Theo Killian: Exploiting the Depmap cancer dependency data using the depmap R package
Mike Smith: Benchmarking compression filters for HDF5 backed matrices
Petr Nazarov: consICA: a package for parallel consensus ICA of multi-omics data and interpretation of the results