09-10, 11:15–11:30 (Europe/Berlin), Main conference room - MW 0350
In the past few years, we have witnessed the exciting development of several single-cell epigenomics methods such as scATAC-seq, scBS-seq or scCUTnRUN/CUTnTag. These new technologies have the potential to enable a quantitative analysis of the epigenetic landscape of cells and resolve tissue heterogeneity. However, despite the rising popularity of single-cell epigenomic protocols, issues related to data analysis could limit their broad adoption among biologists: 1) lack of quality control, normalization, and downstream analysis methods tailored to epigenomic data 2) lack of tools that extend beyond droplet-based scATAC-seq methods, 3) need of significant scripting/programming knowledge. We introduce the Single-Cell Informatics (sincei) toolkit, that tackles the above challenges. sincei provides an easy-to-use, command-line interface for the exploration of data from a wide range of single-cell epigenomics and transcriptomics protocols directly from BAM files. It adopts bulk-epigenomics analysis standards into single-cell genomics workflows and simplifies data integration. sincei is available open-source at https://github.com/bhardwaj-lab/sincei.
I will introduce the novel features of the sincei toolkit, discuss challenges related to epigenomics, and welcome contributions from the community to help build a scalable interaction between sincei and the anndata/mudata structures.
No previous knowledge expected
Vivek is an Assistant professor at the Institute of Biodynamics and Biocomplexity, Utrecht University (Netherlands). His work involves developing computational methods for data analysis from rapidly evolving single-cell genomics/multi-omics techniques, distributing these methods as useful tools for biologists, and training others to do so. The long-term goal of his lab is to enable technologies for in vivo epigenetic reprogramming: https://vblab.org/