Protocol for profiling cell-centric assembled single-cell human transcriptome data in hECA

STAR Protoc. 2022 Jul 31;3(3):101589. doi: 10.1016/j.xpro.2022.101589. eCollection 2022 Sep 16.


Human Ensemble Cell Atlas (hECA) provides a unified informatics framework and the cell-centric-assembled single-cell transcriptome data of 1,093,299 labeled human cells from 116 published datasets. In this protocol, we provide three applications of hECA: "quantitative portraiture" exploration with websites, customizable reference creation for automatic cell type annotation, and "in data" cell sorting with logical conditions. We provide detail steps of connecting to the database, searching cell with conditions, downloading data, and annotating new datasets with customized reference. For complete details on the use and execution of this protocol, please refer to Chen et al. (2022).

Keywords: Bioinformatics; Computer sciences; Gene Expression; RNAseq; Single Cell.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Humans
  • Neoplasm Proteins*
  • Transcriptome* / genetics


  • HECA protein, human
  • Neoplasm Proteins