Systematic comparative analysis of single cell RNA-sequencing methods
By
Jiarui Ding,
Xian Adiconis,
Sean K. Simmons,
Monika S. Kowalczyk,
Cynthia C. Hession,
Nemanja D. Marjanovic,
Travis K Hughes,
Marc H Wadsworth,
Tyler Burks,
Lan T. Nguyen,
John Y. H. Kwon,
Boaz Barak,
William Ge,
Amanda J. Kedaigle,
Shaina Carroll,
Shuqiang Li,
Nir Hacohen,
Orit Rozenblatt-Rosen,
Alex K Shalek,
Alexandra-Chloe Villani,
Aviv Regev,
Joshua Zvi Levin
Posted 09 May 2019
bioRxiv DOI: 10.1101/632216
A multitude of single-cell RNA sequencing methods have been developed in recent years, with dramatic advances in scale and power, and enabling major discoveries and large scale cell mapping efforts. However, these methods have not been systematically and comprehensively benchmarked. Here, we directly compare seven methods for single cell and/or single nucleus profiling from three types of samples – cell lines, peripheral blood mononuclear cells and brain tissue – generating 36 libraries in six separate experiments in a single center. To analyze these datasets, we developed and applied scumi, a flexible computational pipeline that can be used for any scRNA-seq method. We evaluated the methods for both basic performance and for their ability to recover known biological information in the samples. Our study will help guide experiments with the methods in this study as well as serve as a benchmark for future studies and for computational algorithm development.
Download data
- Downloaded 14,069 times
- Download rankings, all-time:
- Site-wide: 489
- In genomics: 29
- Year to date:
- Site-wide: 1,693
- Since beginning of last month:
- Site-wide: 2,325
Altmetric data
Downloads over time
Distribution of downloads per paper, site-wide
PanLingua
News
- 27 Nov 2020: The website and API now include results pulled from medRxiv as well as bioRxiv.
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!