Vivek Bhardwaj
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/
Sessions
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.