Plate IV.205 · Publications
Best practices for single-cell analysis across modalities
Review in Nature Reviews Genetics, 31 March 2023.
Abstract
Recent advances in single-cell technologies have enabled high-throughput molecular profiling of cells across modalities and locations. Single-cell transcriptomics data can now be complemented by chromatin accessibility, surface protein expression, adaptive immune receptor repertoire profiling and spatial information. The increasing availability of single-cell data across modalities has motivated the development of novel computational methods to help analysts derive biological insights. As the field grows, it becomes increasingly difficult to navigate the vast landscape of tools and analysis steps. Here, we summarize independent benchmarking studies of unimodal and multimodal single-cell analysis across modalities to suggest comprehensive best-practice workflows for the most common analysis steps. Where independent benchmarks are not available, we review and contrast popular methods. Our article serves as an entry point for novices in the field of single-cell (multi-)omic analysis and guides advanced users to the most recent best practices.
Cite
@article{heumos2023best,
title = {{Best practices for single-cell analysis across modalities}},
author = {Heumos, Lukas and Schaar, Anna C. and Lance, Christopher and Litinetskaya, Anastasia and Drost, Felix and Zappia, Luke and Lücken, Malte D. and Strobl, Daniel C. and Henao, Juan and Curion, Fabiola and Single-cell Best Practices Consortium and Aliee, Hananeh and Ansari, Meshal and Badia-i-Mompel, Pau and Büttner, Maren and Dann, Emma and Dimitrov, Daniel and Dony, Leander and Frishberg, Amit and He, Dongze and Hediyeh-zadeh, Soroor and Hetzel, Leon and Ibarra, Ignacio L. and Jones, Matthew G. and Lotfollahi, Mohammad and Martens, Laura D. and Müller, Christian L. and Nitzan, Mor and Ostner, Johannes and Palla, Giovanni and Patro, Rob and Piran, Zoe and Ramírez-Suástegui, Ciro and Saez-Rodriguez, Julio and Sarkar, Hirak and Schubert, Benjamin and Sikkema, Lisa and Srivastava, Avi and Tanevski, Jovan and Virshup, Isaac and Weiler, Philipp and Schiller, Herbert B. and Theis, Fabian J.},
journal = {Nature Reviews Genetics},
publisher = {Springer Science and Business Media LLC},
year = {2023},
month = mar,
doi = {10.1038/s41576-023-00586-w},
url = {https://doi.org/10.1038/s41576-023-00586-w},
pmid = {37002403},
pmcid = {PMC10066026}
}