Garching near Munich

 

The 2018 edition of the European Bioconductor Meeting will be hosted at the Technical University of Munich, Germany, on 6-7 December 2018.

Where: TUM-IAS Building, Lichtenbergstrasse 2a, Garching
When: 6 - 7 December 2018
On twitter: #EuroBioc2018

Introduction

The meeting is aimed at biologists, bioinformaticians, statisticians, programmers and software engineers who use or contribute to the Bioconductor project, or are interested in using Bioconductor. The goals are to:

- foster the exchange of technical expertise
- keep contributors up to speed with the latest developments coordinate any related efforts.

Confirmed invited speakers

Keegan Korthauer, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health
Fanny Perraudeau, Whole Biome, San Francisco
Bernd Bischl, LMU, Munich

Schedule

Thu 6 Dec TUM-IAS Building, Lichtenbergstrasse 2a, Garching
09:00 - 09:15 Registration
09:15 - 09:30 Welcome and introduction
09:30 - 10:00 Bernd Bischl mlr3: Towards an object-oriented, configurable ML pipeline system in R6

10:00 - 10:30 Session I
10:00 - 10:15 Lukas Weber: HDCytoData package: High-dimensional cytometry benchmark datasets in Bioconductor formats
10:15 - 10:30 Elena Landoni: Normalization and batch correction effects on class comparison analysis with high throughput data: a simulation study
10:30 - 11:00 Coffee break

11:00 - 12:15 Session II - Visualization
11:00 - 11:15 Nemanja Vucic: Using R/Shiny implementation of Bioconductor packages on the Cancer Genomic Cloud platform
11:15 - 11:30 Federico Marini: iSEE: data exploration made easy & reproducible
11:30 - 11:45 Svetlana Ovchinnikova / Simon Anders: R/LinkedCharts: A novel approach for simple but powerful interactive data analysis
11:45 - 12:00 Laurent Gatto / Lisa Breckels: Interactive visualisation of spatial proteomics data
12:00 - 12:15 Phil Cheng: TCGA Browser
12:15 - 13:30 Lunch
13:30 - 14:00 Martin Morgan Update from the Bioconductor core team

14:00 - 15:00 Session III - Epigenomics
14:00 - 14:15 Shijie Zheng: Identification of differentially methylated cell-types in Epigenome-Wide Association Studies
14:15 - 14:30 Jonas Ibn-Salem: sevenC: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
14:30 - 14:45 Markus List: Analysing large-scale epigenomic data with DeepBlue
14:45 - 15:00 Yadollah Shahryary Dizaji: MethylStar: An efficient and flexible pipeline for population-level analysis of Whole Genome Bisulfite Sequencing (WGBS) data
15:00 - 15:15 Alexander Gosdschan: methylKit, a package for DNA methylation analysis from high-throughput bisulfite sequencing data
15:15 - 15:45 Coffee break

15:45 - 17:00 Session IV - Proteomics
15:45 - 16:00 Christian Panse: rawDiag: access orbitrap data on the fast lane
16:00 - 16:15 Nils Kurzawa: TPP: a Bioconductor package for analysis of thermal proteome profiling experiments
16:15 - 16:30 Markus Gruber: MS-EmpiRe - Mass Spectrometry analysis using Empirical and Replicate based statistics
16:30 - 16:45 Helena Crowell: Differential discovery in CyTOF data with CATALYST & diffcyt
16:45 - 17:00 Constantin Ahlmann-Eltze: Empirical Bayesian Modeling for Mass Spectrometry Data
18:00 - 19:00 Free time (Christmas market)
19:30 - Dinner at Hofbrauhaus (self-funded)

Fri 7 Dec TUM-IAS Building, Lichtenbergstrasse 2a, Garching
09:00 - 09:30 Keegan Korthauer Practical recommendations for controlling false discoveries in computational biology

09:30 - 10:15 Session V
09:30 - 09:45 Ruizhu Huang: The tree aggregation
09:45 - 10:00 Thomas Girke: signatureSearch: Gene Expression Signature Search Methods for Discovering Novel Modes of Action of Drugs and Other Cellular Perturbations
10:00 - 10:15 Ludwig Geistlinger: Towards a gold standard for benchmarking gene set enrichment analysis
10:15 - 10:45 Coffee break

10:45 - 12:00 Session VI - Multiomics
10:45 - 11:00 Vince Carey: Hybrid data architectures for multiomic experiments
11:00 - 11:15 Johannes Rainer: ensembldb: coordinate mapping between the genome, exome, transcriptome and proteome
11:15 - 11:30 Laurent Gatto: A Grammar of Omics Data Manipulation
11:30 - 11:45 Leo Lahti: A roadmap for microbiome bioinformatics in R
11:45 - 12:00 Katarzyna Wreczycka: Genomation: a toolkit to summarize, annotate and visualize genomic intervals
12:00 - 13:30 Lunch
13:30 - 14:00 Fanny Perraudeau Unlocking RNA-seq tools for zero-inflation and single cell applications using ZINB-WaVE observation weights

14:00 - 15:30 Session VII - RNA
14:00 - 14:15 Clara Benoit-Pilven: kissDE retrieves condition-specific variants in RNA-Seq data from model and non-model species
14:15 - 14:30 Charlotte Soneson: A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs
14:30 - 14:45 Christian Mertes: OUTRIDER: A statistical method for detecting aberrantly expressed genes in RNA sequencing data
14:45 - 15:00 Svetozar Nesic: Targeted synthetic datasets to benchmark allele specific expression algorithms
15:00 - 15:15 Marijke Van Moerbeke: A Random Effects Model for the Identification of Differential Splicing (REIDS) Using Exon and HTA Arrays
15:15 - 15:30 Ziga Avsec: Kipoi: accelerating the community exchange and reuse of predictive models for genomics
15:30 - 15:35 Wrap-up and closing

 

Organising committee

Wolfgang Huber, European Microbiology Laboratory (EMBL), Heidelberg
Martin Morgan, Roswell Park Comprehensive Cancer Center, Buffalo
Mark Robinson, University of Zurich
Julien Gagneur, Technical University of Munich
Anne-Laure Boulesteix, Ludwig-Maximilians Universitaet, Munich
Fabian Theis, Helmholtz Zentrum Munich