Workshops

Long workshop: Trajectory inference across conditions: differential expression and differential progression

Trajectory inference across conditions: differential expression and differential progression Hector Roux de Bezieux, Kelly Street, Koen Van den Berge University of California, Berkeley Abstract In single-cell RNA-sequencing (scRNA-seq), gene expression is assessed individually for each cell, allowing the investigation of developmental processes, such as embryogenesis and cellular differentiation and regeneration, at unprecedented resolutions. In such dynamic biological systems, grouping cells into discrete groups is not reflective of the biology. Cellular states rather form a continuum, e.

Long workshop: systemPipe: Workflow and Visualization Toolkit

systemPipe: Workflow and Visualization Toolkit Daniela Cassol, Le Zhang, Thomas Girke Institute for Integrative Genome Biology, University of California, Riverside, California, USA. Abstract This workshop introduces systemPipe (SP), a generic toolkit for designing and running reproducible data analysis workflows. The environment consists of three major modules implemented as R/Bioconductor packages. systemPipeR (SPR) provides core functionalities for defining workflows, interacting with command-line software, and executing both R and/or command-line software, as well as generating publication-quality analysis reports.

Long workshop: Reproducing a single-cell proteomics data analysis using QFeatures and scp

Reproducing a single-cell proteomics data analysis using QFeatures and scp Christophe Vanderaa, Laurent Gatto UCLouvain Abstract Recent advances in sample preparation, processing and mass spectrometry (MS) have enabled the emergence of MS-based single-cell proteomics (SCP). QFeatures along with its extension scp allow for standardized analysis of SCP data. QFeatures is based on the SummarizedExperiment and MultiAssayExperiment Bioconductor classes. Assays in a QFeatures object have a hierarchical relation: proteins are composed of peptides, themselves produced by spectra.

Long workshop: Multi-omic Integration of cBioPortal and TCGA data with MultiAssayExperiment

Multi-omic Integration of cBioPortal and TCGA data with MultiAssayExperiment Marcel Ramos, Levi Waldron, Ludwig Geistlinger CUNY Graduate School of Public Health and Health Policy Abstract This workshop demonstrates the leveraging of public multi-omics databases, such as cBioPortal and The Cancer Genome Atlas (TCGA), through an overview of the cBioPortalData and curatedTCGAData experiment data packages. It introduces users to minimal data management with MultiAssayExperiment and TCGAutils, packages that organize and manage multi-omics datasets.

Long workshop: Introduction to the Terra/AnVIL Cloud-based Genomics Platform

Introduction to the Terra/AnVIL Cloud-based Genomics Platform Sehyun Oh, Levi Waldron The City University of New York Abstract The rapidly growing size of genomic datasets introduces challenges of data transfer, storage, access, sharing, and computing. In this workshop, we introduce cloud-based genomics platform Terra as a potential solution. Terra hosts large-scale genomic and genomic-related data sets and provide secure remote access to them and to individually uploaded data resources. Terra also provides on-demand computational capacity through Google Cloud Platform (GCP), and interactive analysis interfaces such as Jupyter notebook and RStudio.

Long workshop: Introduction to Bioconductor annotation resources

Introduction to Bioconductor annotation resources James MacDonald University of Washington Abstract There are various annotation packages provided by the Bioconductor project that can be used to incorporate additional information to results from high-throughput experiments. This can be as simple as mapping Ensembl IDs to corresponding HUGO gene symbols, to much more complex queries involving multiple data sources. In this workshop we will cover the various classes of annotation packages, what they contain, and how to use them efficiently.

Long workshop: Interfacing Bioconductor with tidyverse with tidySingleCellExperiment and tidySummarisedExperiment

Interfacing Bioconductor with tidyverse with tidySingleCellExperiment and tidySummarisedExperiment Stefano Mangiola, Maria Doyle WEHI Abstract Recently, plyranges and tidybulk represented efforts toward the harmonization of transcriptomic data structures and workflows using the concept of data tidiness, to facilitate modularisation. In this workshop, we present tidySingleCellExperiment and tidySummarizedExperiment, two R packages that allow the user to visualise and manipulate SingleCellExperiment and SummarizedExperiment objects in a tidy fashion. Importantly, the framework tidybulk now works natively with SummarizedExperiment objects and, thanks to tidySummarizedExperiment, allow tidy and modular RNA sequencing analyses without renouncing to the efficiency of Bioconductor data containers.

Long workshop: Epidemiology for Bioinformaticians

Epidemiology for Bioinformaticians Chloe Anya Mirzayi, Levi Waldron CUNY Graduate School of Public Health and Health Policy Abstract Concepts of causal inference in epidemiology have important ramifications for studies across bioinformatics and other fields of health research. In this workship, we introduce basic concepts of epidemiology, study design, and causal inference for bioinformaticians. Emphasis is placed on addressing bias and confounding as common threats to assessing a causal pathway in a variety of study design types and when using common forms of analyses such as GWAS and survival analysis.

Long workshop: Effectively using the DelayedArray framework to support the analysis of large datasets

Effectively using the DelayedArray framework to support the analysis of large datasets Peter Hickey Walter and Eliza Hall Institute of Medical Research Abstract This workshop gives an introductory overview of the DelayedArray framework, which can be used by R / Bioconductor packages to support the analysis of large array-like datasets. A DelayedArray is like an ordinary array in R, but allows for the data to be in-memory, on-disk in a file, or even hosted on a remote server.

Long workshop: Dimension Reduction for Beginners

Dimension Reduction for Beginners Aedin Culhane Dana-Farber Cancer Institute / Harvard University Abstract This workshop will provide a beginner’s guide to dimension reduction, principal component analysis (PCA), the difference between singular value decomposition, different forms of PCA and fast PCA versions for single-cell data analysis. We will describe how to detect artifacts and select the optimal number of components. It will focus on SVD, PCA, CA, TSNE and UMAP applied single-cell data.

Long workshop: Building Carpentries-based Bioconductor Lessons

Building Carpentries-based Bioconductor Lessons Jenny Drnevich, Charlotte Soneson, Toby Hodges, Laurent Gatto University of Illinois, Urbana-Champaign Abstract The Bioconductor teaching committee was established in early 2020, and one of its aims is to coordinate the development of Bioconductor-focused training material, consistent with the guiding principles of the Carpentries (https://carpentries.org). During its first year, the committee has started the development of three lessons: an introduction to R (with a Bioconductor focus), an overview of the Bioconductor project, and a lesson on bulk RNA-seq analysis with Bioconductor.