APEC: an accesson-based method for single-cell chromatin accessibility analysis

被引：15

作者：

Li, Bin ^{[1
]}

Li, Young ^{[1
]}

Li, Kun ^{[1
]}

Zhu, Lianbang ^{[1
]}

Yu, Qiaoni ^{[1
]}

Cai, Pengfei ^{[1
]}

Fang, Jingwen ^{[1
,2
]}

Zhang, Wen ^{[1
]}

Du, Pengcheng ^{[1
]}

Jiang, Chen ^{[1
]}

Lin, Jun ^{[1
]}

Qu, Kun ^{[1
,3
]}

机构：

[1] Univ Sci & Technol China, Affiliated Hosp 1, Hefei Natl Lab Phys Sci Microscale, Div Life Sci & Med,Div Mol Med,Dept Oncol, Hefei 230001, Anhui, Peoples R China

[2] HanGene Biotech, Xiaoshan Innovat Polis, Hangzhou 3CAS, Zhejiang, Peoples R China

[3] Univ Sci & Technol China, CAS Ctr Excellence Mol Cell Sci, CAS Key Lab Innate Immun & Chron Dis, Hefei 230027, Anhui, Peoples R China

来源：

GENOME BIOLOGY | 2020年 / 21卷 / 01期

基金：

国家重点研发计划; 中国国家自然科学基金;

关键词：

scATAC-seq; Cell clustering; Accesson; Regulome; Pseudotime trajectory; RNA-SEQ; TRANSCRIPTION FACTORS; REVEALS PRINCIPLES; STEM-CELLS; CTCF; GENOME; THYMOCYTES; EXPRESSION; LANDSCAPE; APOPTOSIS;

D O I：

10.1186/s13059-020-02034-y

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

The development of sequencing technologies has promoted the survey of genome-wide chromatin accessibility at single-cell resolution. However, comprehensive analysis of single-cell epigenomic profiles remains a challenge. Here, we introduce an accessibility pattern-based epigenomic clustering (APEC) method, which classifies each cell by groups of accessible regions with synergistic signal patterns termed "accessons". This python-based package greatly improves the accuracy of unsupervised single-cell clustering for many public datasets. It also predicts gene expression, identifies enriched motifs, discovers super-enhancers, and projects pseudotime trajectories. APEC is available at .

引用

页数：27

共 84 条

[1] Identification of Flt3+ lympho-myeloid stem cells lacking erythro-megakaryocytic potential:: A revised road map for adult blood lineage commitment [J].