We have located links that may give you full text access.
Automatic quality control of single-cell and single-nucleus RNA-seq using valiDrops.
NAR genomics and bioinformatics. 2023 December
Single-cell and single-nucleus RNA-sequencing (sxRNA-seq) measures gene expression in individual cells or nuclei enabling comprehensive characterization of cell types and states. However, isolation of cells or nuclei for sxRNA-seq releases contaminating RNA, which can distort biological signals, through, for example, cell damage and transcript leakage. Thus, identifying barcodes containing high-quality cells or nuclei is a critical analytical step in the processing of sxRNA-seq data. Here, we present valiDrops, an automated method to identify high-quality barcodes and flag dead cells. In valiDrops, barcodes are initially filtered using data-adaptive thresholding on community-standard quality metrics, and subsequently, valiDrops uses a novel clustering-based approach to identify barcodes with distinct biological signals. We benchmark valiDrops and show that biological signals from cell types and states are more distinct, easier to separate and more consistent after filtering by valiDrops compared to existing tools. Finally, we show that valiDrops can predict and flag dead cells with high accuracy. This novel classifier can further improve data quality or be used to identify dead cells to interrogate the biology of cell death. Thus, valiDrops is an effective and easy-to-use method to improve data quality and biological interpretation. Our method is openly available as an R package at www.github.com/madsen-lab/valiDrops.
Full text links
Related Resources
Get seemless 1-tap access through your institution/university
For the best experience, use the Read mobile app
All material on this website is protected by copyright, Copyright © 1994-2024 by WebMD LLC.
This website also contains material copyrighted by 3rd parties.
By using this service, you agree to our terms of use and privacy policy.
Your Privacy Choices
You can now claim free CME credits for this literature searchClaim now
Get seemless 1-tap access through your institution/university
For the best experience, use the Read mobile app