Bioconductor

Conference home
Registration
Call for submissions

Schedule
- Key dates
- Confirmed Speakers
- Conference Schedule
- Workshops
- Abstracts

Resources
- Code of conduct
- Previous EuroBioc meetings
- Organizing committee

Conference Sponsors

R Consortium F1000 Research Dept. of Statistical Sciences, University of Padova

Patronage

Dept. of Biology, University of Padova

Bioconductor: https://bioconductor.org
Hosted on GitHub Pages
Theme by orderedlist

European Bioconductor Meeting 2020

Conference programme

The conference will take place on 14-18 December 2020, from 14:00 to 20:00 CET.

Bird’s eye view of the schedule

Monday 14 December

Time Speaker
14:00 - 14:10 Welcome and opening remarks
14:10 - 14:30 Martin Morgan - The Bioconductor Project: Updates and Directions
14:30 - 14:45 Kevin Rue-Albrecht - BiocChallenges presentation
14:45 - 15:30 Keynote: Holger Heyn - A spatially-resolved tumor immune cell atlas for precision immuno-oncology
15:30 - 15:40 Break
15:40 - 16:05 Simone Tiberi - distinct: a novel approach to differential analyses
16:05 - 16:15 Break
16:15 - 17:00 Keynote: Sehyun Oh - Bioinformatics On Cloud: How to leverage cloud-based resources for your bioinformatics works
17:00 - 17:15 Break
17:15 - 17:25 Pierre-Luc Germain - Doublet identification and characterization in single-cell data with scDblFinder
17:25 - 17:35 Andrea Sottosanti - A new statistical approach for the simultaneous clustering of genes and cells in spatial transcriptomic experiments
17:35 - 17:45 Kwame Forbes - Integration of preprocessed single-cell datasets with bulk differential analysis results for DESeq2
17:45 - 17:55 Brenda Pardo - Using VisiumExperiment objects at spatialLIBD package
17:55 - 18:05 Break
18:05 - 18:15 Federico Marini - annoFuse and shinyFuse: Annotating, prioritizing, and interactively exploring putative oncogenic RNA fusions
18:15 - 18:25 Rory Stark - Normalizing ChIP and ATAC sequencing data for differential analysis
18:25 - 18:35 Reka Toth - Methrix: a package for systematic aggregation and analysis of bisulfite sequencing data
18:35 - 18:45 Ricardo Omar Ramirez Flores - Decoupling statistics and networks: a crowdsourced systematic assessment of transcription factor activity estimation from transcriptomics data
18:45 - 19:00 Break
19:00 - 20:00 Birds of a feather 1: Infrastructure to enable spatially resolved transcriptomics data analysis with Bioconductor (Dario Righelli)
  Birds of a feather 2: Creating Github Actions for building and checking Bioconductor Packages (Mike Smith)

Tuesday 15 December

Time Speaker
14:00 - 14:45 Keynote: Britta Velten - Integrative analysis of multi-omics data
14:45 - 14:55 Break
14:55 - 15:20 Angela Andreella - pARI package: valid double-dipping via permutation-based All Resolutions Inference
15:20 - 15:30 Break
15:30 - 15:40 Thomas Schwarzl - DEWSeq: a new data analysis package for eCLIP data showing improved RNA-binding site assignments for the ENCODE eCLIP data
15:40 - 15:50 David Zhang - dasper: Detection of aberrant splicing events from RNA-sequencing data
15:50 - 16:00 Ying Chen - bambu: reference-guided transcript discovery and quantification for long read RNA-Seq data
16:00 - 16:10 Mattia Furlan - Inference of transcriptional and post-transcriptional dynamics from sequencing experiments
16:10 - 16:20 Louise Huuki - Correcting for Cell RNA Fractions in MDD RNA-seq Data
16:20 - 16:30 Break
16:30 - 18:00 Long Workshop 1: Stefano Mangiola - tidytranscriptomics : introduction to tidy analysis of single-cell and bulk RNA sequencing data
  Long Workshop 2: Rory Stark - Quantitiative analysis of ChiP-seq, ATAC-seq, and related DNA enrichment assays
18:00 - 18:15 Break
18:15 - 19:15 Poster Session
19:15 - 20:00 Short Workshop 1: Marcel Ramos - Multi-omic Integration and Analysis of cBioPortal and TCGA data with MultiAssayExperiment
  Short Workshop 2: Federico Agostinis - NewWave, new R package for dimensional reduction and batch effect removal for single cell RNA-seq data

Wednesday 16 December

Time Speaker
14:00 - 14:15 Announcement: Wolfgang Huber
14:15 - 15:00 Keynote: Monica Chiogna - Connections matter: a conversation between statistics and biology
15:00 - 15:10 Break
15:10 - 15:35 Alejandro Reyes - Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer
15:35 - 16:00 Elyas Heidari - scGCN: A Geometric Deep Learning Framework on Single-cell Gene Networks
16:00 - 16:10 Break
16:10 - 16:20 Elisa Salviato - SourceSet: a graphical model approach to identify primary genes in perturbed biological pathways
16:20 - 16:30 Christian Holland - Estimation of transcription factor and pathway activities from bulk and single-cell transcriptomics data with dorothea and progeny
16:30 - 16:40 Alejandro Cisterna García - Switching between mendelian genes space and clinical phenotypes space contributes to comparative Mendelian gene sets analysis
16:40 - 16:50 Leo Lahti - MicrobiomeExperiment: a new class for microbiome data
16:50 - 17:00 Valeria Policastro - ROBIN (ROBustness In Network): for Comparison and Validation of communities
17:00 - 17:10 Matteo Calgaro - Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data
17:10 - 17:20 Riccardo Corradin - BNPmix: an R package to estimate Bayesian nonparametric mixtures
17:20 - 17:30 Break
17:30 - 18:15 Short Workshop 3: Spiro C Stilianoudakis - preciseTAD: a machine-learning framework for predicting boundaries of 3D genomic elements
  Short Workshop 4: Dario Righelli - Spatial Transcriptomics workflow using SpatialExperiment package classes
18:15 - 18:30 Break
18:30 - 20:00 Long Workshop 3: Nicholas J Eagles - SPEAQeasy: a Scalable Pipeline for Expression Analysis and Quantification for R/Bioconductor-powered RNA-seq analyses
  Long Workshop 4: iSEE: Interactive SummarizedExperiment Explorer

Thursday 17 December

Time Speaker
13:30 - 14:00 After-lunch informal coffee break
14:00 - 14:45 Keynote: Nicola Segata - Large-scale high-resolution metagenomics: methods, data, infrastructure
14:45 - 14:55 Break
14:55 - 15:20 Etienne Becht - Infinity Flow: High-throughput single-cell quantification of 100s of proteins using conventional flow cytometry and machine learning
15:20 - 15:30 Break
15:30 - 16:15 Keynote: Elsa Bernard - Population Genomics and Personalized Prognosis in Myelodysplastic Syndromes
16:15 - 16:25 Break
16:25 - 16:50 Abby Spangler - Evaluation of cell populations in the locus coeruleus through spatial transcriptomics
16:50 - 17:00 Mike Smith - Browsing and searching the Bioconductor codebase
17:00 - 17:10 Charlotte Soneson - The Bioconductor teaching committee: A collaborative effort to consolidate Bioconductor-focused training material and establish a community of trainers
17:10 - 17:20 Naji Faris - “Empower” the Biologist and “liberate” the Bioinformatician
17:20 - 17:30 Break
17:30 - 18:15 Short Workshop 5: Laurent Gatto - QFeatures: Quantitative features for mass spectrometry data
  Short Workshop 6: Mahmoud Ahmed - Integration of ChIP-seq and RNA-seq data in R
18:15 - 18:30 Break
18:30 - 19:15 Short Workshop 7: Johannes Rainer - Seamless Integration of Mass Spectrometry Data from Different Sources with the Spectra Package
18:30 - 20:00 Long Workshop 5: Hector Roux de Bezieux - Trajectory inference across conditions: differential expression and differential progression

Friday 18 December

Time Speaker
13:30 - 14:00 After-lunch informal coffee break
14:00 - 14:45 Keynote: Luke Zappia - Interoperability between Bioconductor and Python for scRNA-seq analysis
14:45 - 14:55 Break
14:55 - 15:05 Chen Meng - Interactive and comprehensive exploration of ExpressionSet using ExpressionSetViewer
15:05 - 15:15 Alan Brian O’Callaghan - Scalable or density-preserving (but not both) non-linear dimensionality reduction with snifter and densvis
15:15 - 15:25 Maria Dermit - Peptide Correlation Analysis (PeCorA) Reveals Differential Proteoform Regulation
15:25 - 15:35 Witold Wolski - Prolfqua - R package for proteomics label-free quantification
15:35 - 15:45 Anne-Maud Ferreira - CyTOF data analysis workflow with Bioconductor packages
15:45 - 15:55 Pol Castellano Escuder - POMA: An user-friendly workflow for pre-processing and statistical analysis of mass spectrometry data
15:55 - 16:05 Break
16:05 - 16:30 Christophe Vanderaa - Standardised and reproducible analysis of mass spectrometry-based single-cell proteomics data
16:30 - 16:55 Oliver Crook - The effect of phosphorylation on the spatial proteome
16:55 - 17:05 Break
17:05 - 18:05 Birds of a feather 3: The emerging R ecosystem for microbiome research (Leo Lahti)
  Birds of a feather 4: Ten simple rules for thriving in bioinformatics research (Federico Marini)
18:05 - 18:20 Break
18:20 - 19:05 Keynote: Henrik Bengtsson - Future: Simple, Extendable, Generic Framework for Parallel Processing in R
19:05 - 19:15 Kevin Rue-Albrecht - BiocChallenges closing
19:15 - 19:20 Closing remarks
19:20 - 19:25 Announcements

Posters