Document Type

Article

Publication Date

6-1-2020

Keywords

JGM, JAXCC

JAX Source

Bioinformatics 2020 Jun 1; 36(11):3582-3584

PMID

32119082

DOI

https://doi.org/10.1093/bioinformatics/btaa128

Grant

GM124922,Chan- Zuckerberg Initiative and Silicon Valley Community Foundation

Abstract

SUMMARY: Single-cell RNA-sequencing (scRNA-seq) technology enables studying gene expression programs from individual cells. However, these data are subject to diverse sources of variation, including 'unwanted' variation that needs to be removed in downstream analyses (e.g. batch effects) and 'wanted' or biological sources of variation (e.g. variation associated with a cell type) that needs to be precisely described. Surrogate variable analysis (SVA)-based algorithms, are commonly used for batch correction and more recently for studying 'wanted' variation in scRNA-seq data. However, interpreting whether these variables are biologically meaningful or stemming from technical reasons remains a challenge. To facilitate the interpretation of surrogate variables detected by algorithms including IA-SVA, SVA or ZINB-WaVE, we developed an R Shiny application [Visual Surrogate Variable Analysis (V-SVA)] that provides a web-browser interface for the identification and annotation of hidden sources of variation in scRNA-seq data. This interactive framework includes tools for discovery of genes associated with detected sources of variation, gene annotation using publicly available databases and gene sets, and data visualization using dimension reduction methods.

AVAILABILITY AND IMPLEMENTATION: The V-SVA Shiny application is publicly hosted at https://vsva.jax.org/ and the source code is freely available at https://github.com/nlawlor/V-SVA.

CONTACT: leed13@miamioh.edu or duygu.ucar@jax.org.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Comments

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License

Share

COinS