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科学家研发可用于整合单细胞染色质可及性分析的ArchR可扩展软件包
2021-02-27 22:13

研发出用于整合单细胞染色质可及性分析的ArchR可扩展软件包,这一成果由美国斯坦福大学医学院William J. Greenleaf、Howard Y. Chang和Jeffrey M. Granja课题组合作经过不懈努力而取得。相关论文发表在2021年2月25日出版的《自然-遗传学》杂志上。

在本研究中,研究人员介绍了可用于调控染色质单细胞分析的R软件包(ArchR; https://www.archrproject.com/),该软件包可以快速、全面地分析单细胞染色质可及性数据。 ArchR为复杂的单细胞分析提供了直观的、以用户为中心的界面,包括双峰去除、单细胞聚类和细胞类型识别、统一的峰集生成、细胞轨迹识别、DNA元件与基因的连接、转录因子足迹、通过染色质可及性和与单细胞RNA测序(scRNA-seq)的多基因组整合预测mRNA表达水平。

利用标准Unix笔记本电脑可以在8小时内分析超过120万个单细胞,ArchR是一个完整的软件包,可对单细胞染色质可及性进行端到端分析,从而有助于在单细胞水平理解基因调控。

研究人员表示,单细胞染色质可及性分析有利于基因调控图谱的绘制,但缺乏可从这些数据中快速挖掘生物学功能的可扩展软件。

附:英文原文

Title: ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

Author: Jeffrey M. Granja, M. Ryan Corces, Sarah E. Pierce, S. Tansu Bagdatli, Hani Choudhry, Howard Y. Chang, William J. Greenleaf

Issue&Volume: 2021-02-25

Abstract: The advent of single-cell chromatin accessibility profiling has accelerated the ability to map gene regulatory landscapes but has outpaced the development of scalable software to rapidly extract biological meaning from these data. Here we present a software suite for single-cell analysis of regulatory chromatin in R (ArchR; https://www.archrproject.com/) that enables fast and comprehensive analysis of single-cell chromatin accessibility data. ArchR provides an intuitive, user-focused interface for complex single-cell analyses, including doublet removal, single-cell clustering and cell type identification, unified 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 single-cell RNA sequencing (scRNA-seq). Enabling the analysis of over 1.2 million single cells within 8h on a standard Unix laptop, ArchR is a comprehensive software suite for end-to-end analysis of single-cell chromatin accessibility that will accelerate the understanding of gene regulation at the resolution of individual cells.

DOI: 10.1038/s41588-021-00790-6

Source: https://www.nature.com/articles/s41588-021-00790-6

Nature Genetics:《自然—遗传学》,创刊于1992年。隶属于施普林格·自然出版集团,最新IF:41.307
官方网址:https://www.nature.com/ng/
投稿链接:https://mts-ng.nature.com/cgi-bin/main.plex


本期文章:《自然—遗传学》:Online/在线发表

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