Infrastructure programmings

Short talk: ORCESTRA: Web application for orchestrating and sharing large multimodal data for transparent and reproducible research

ORCESTRA: Web application for orchestrating and sharing large multimodal data for transparent and reproducible research Anthony Mammoliti,Minoru Nakano University Health Network Abstract Reproducibility is essential to open science, as there is limited relevance for findings that can not be reproduced by independent research groups, regardless of its validity. It is therefore crucial for scientists to describe their experiments in sufficient detail so they can be reproduced, scrutinized, challenged, and built upon.

Short talk: Managing and running conda packages through R with the Herper package

Managing and running conda packages through R with the Herper package Matt Paul,Doug Barrows,Tom Carroll The Rockefeller University Abstract Many tools for data analysis are not available in R, but are present in public repositories like conda. In this workshop we will demonstrate the Herper package and its comprehensive set of functions to interact with the conda package management system. With Herper users can install, manage and run conda packages from the comfort of their R session.

Short talk: ExperimentSubset: An R package to manage subsets of Bioconductor Experiment objects

ExperimentSubset: An R package to manage subsets of Bioconductor Experiment objects Irzam Sarfraz,Muhammad Asif,Joshua D. Campbell National Textile University, Faisalabad, Pakistan & Boston University School of Medicine, Boston, MA, USA Abstract R Experiment objects such as the SummarizedExperiment or SingleCellExperiment are data containers for storing one or more matrix-like assays along with associated row and column data. These objects have been used to facilitate the storage and analysis of high-throughput genomic data generated from technologies such as single-cell RNA sequencing.

Short talk: atena: analysis of transposable elements in R and Bioconductor

atena: analysis of transposable elements in R and Bioconductor Beatriz Calvo-Serra,Robert Castelo Dept. of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain Abstract Transposable elements (TEs) are DNA sequences that can mobilize within the genome either through a DNA intermediate, and hence those are known as class II TEs or DNA transposons, or through an RNA intermediate, which are known as class I TEs or retrotransposons, as in the case of endogenous retroviruses (ERVs).