Schep Alicia N, Wu Beijing, Buenrostro Jason D, Greenleaf William J
Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.
Center for Personal Dynamic Regulomes, Stanford University, Stanford, California, USA.
Nat Methods. 2017 Oct;14(10):975-978. doi: 10.1038/nmeth.4401. Epub 2017 Aug 21.
Single-cell ATAC-seq (scATAC) yields sparse data that make conventional analysis challenging. We developed chromVAR (http://www.github.com/GreenleafLab/chromVAR), an R package for analyzing sparse chromatin-accessibility data by estimating gain or loss of accessibility within peaks sharing the same motif or annotation while controlling for technical biases. chromVAR enables accurate clustering of scATAC-seq profiles and characterization of known and de novo sequence motifs associated with variation in chromatin accessibility.
单细胞染色质转座酶可接近性测序（scATAC）产生的数据较为稀疏，这使得传统分析颇具挑战性。我们开发了chromVAR（http://www.github.com/GreenleafLab/chromVAR），这是一个R软件包，用于通过估计共享相同基序或注释的峰内可接近性的增加或减少，同时控制技术偏差，来分析稀疏的染色质可接近性数据。chromVAR能够对scATAC测序图谱进行准确聚类，并对与染色质可接近性变化相关的已知和新生序列基序进行表征。
