Recent methodological advances have increased the throughput of scATAC-seq, enabling a single lab to generate data from hundreds of thousands of cells on the timescale of weeks 5, 6, 8. These chromatin-based assays have illuminated cell type-specific biology and provided insights into complex biological processes previously hidden by ensemble averaging 3– 7. The advent of single-cell approaches for the assay for transposase-accessible chromatin using sequencing (scATAC-seq) has made it possible to study chromatin accessibility and gene regulation in single cells 1, 2. Single-cell approaches have revolutionized our understanding of biology, opening the door for a wide array of applications ranging from interrogation of cellular heterogeneity to identification of disease-specific processes. Enabling the analysis of over 1.2 million single cells within 8 hours on a standard Unix laptop, ArchR is a comprehensive analytical suite for end-to-end analysis of single-cell chromatin accessibility data that will accelerate the understanding of gene regulation at the resolution of individual cells. ArchR provides an intuitive, user-focused interface for complex single-cell analyses including doublet removal, single-cell clustering and cell type identification, robust peak set generation, cellular trajectory identification, DNA element to gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility, and multi-omic integration with scRNA-seq. Here we present a software suite for single-cell analysis of regulatory chromatin in R (ArchR that enables fast and comprehensive analysis of single-cell chromatin accessibility data. The advent of large-scale single-cell chromatin accessibility profiling has accelerated our ability to map gene regulatory landscapes, but has outpaced the development of robust, scalable software to rapidly extract biological meaning from these data.
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