ScBatch: batch-effect correction of RNA-seq data through sample distance matrix adjustment.
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ABSTRACT: Motivation
Batch effect is a frequent challenge in deep sequencing data analysis that can lead to misleading conclusions. Existing methods do not correct batch effects satisfactorily, especially with single-cell RNA sequencing (RNA-seq) data.Results
We present scBatch, a numerical algorithm for batch-effect correction on bulk and single-cell RNA-seq data with emphasis on improving both clustering and gene differential expression analysis. scBatch is not restricted by assumptions on the mechanism of batch-effect generation. As shown in simulations and real data analyses, scBatch outperforms benchmark batch-effect correction methods.Availability and implementation
The R package is available at github.com/tengfei-emory/scBatch. The code to generate results and figures in this article is available at github.com/tengfei-emory/scBatch-paper-scripts.Supplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Fei T
PROVIDER: S-EPMC7214039 | biostudies-literature |
REPOSITORIES: biostudies-literature
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