SpatialQC: automated quality control for spatial transcriptome data.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 39051702.
- Also identified by DOI 10.1093/bioinformatics/btae458 and PMC identifier 11333854.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
The advent of spatial transcriptomics has revolutionized our understanding of the spatial heterogeneity in tissues, providing unprecedented insights into the cellular and molecular mechanisms underlying biological processes. Although quality control (QC) critical for downstream data analyses, there is currently a lack of specialized tools for one-stop spatial transcriptome QC. Here, we introduce SpatialQC, a one-stop QC pipeline, which generates comprehensive QC reports and produces clean data in an interactive fashion. SpatialQC is widely applicable to spatial transcriptomic techniques. source code and user manuals are available via https://github.com/mgy520/spatialQC, and deposited on Zenodo (https://doi.org/10.5281/zenodo.12634669).
Medical subject headings
- Quality Control
- Software
- Transcriptome