Last modified: 7 July, 2022

This package provides an ‘Orchestra’ environment for exploring the hca and cellxgenedp packages for Human Cell Atlas data access. Please see the vignettes for more information.


This short workshop demonstrates how three R/Bioconductor packages provide access to the increasing number of single cell gene expression data sets produced as part of the Human Cell Atlas. The cellxgenedp package ( allows discovery, download for import into R / Bioconductor as SingleCellExperiment objects, and visual exploration through the cellxgene data portal of more than 300 consistently-processed datasets. The hca package ( provides additional, fine-grained, access to 208 projects, including 50 that have been processed by standard Human Cell Atlas workflows defined in WDL (Workflow Description Language). Description of the processing workflow in WDL means that other datasets, including those produced by individual labs, can be consistently processed from fastq or bam files to objects that are easily integrated into R / Bioconductor work flows. This process is particularly easy when performed in the AnVIL computational cloud, a process facilitated by the AnVIL ( package.


This workshop assumes familiarity with single-cell RNAseq experiments, especially the ‘count matrix’ summary of gene x cell expression values.

The software in this workshop uses dplyr and ‘tidy’ representations for working the R data.frame-like data.

The workshop introduces the SingleCellExperiment data representation, without emphasizing the mechanical aspects of working with data in this format.

A portion of the workshop uses the AnVIL computational cloud. Actual use of the cloud (rather than ‘following along’ during the presentation) requires some familiarity with Google cloud computing concepts related to billing; some familiarity with cloud concepts such as storage buckets and compute engines will also be helpful.


This vignette forms the basis of the workshop presentation. Participants can ‘follow along’ during the presentation, work through detailed steps after the workshop, and explore avenues suggested by the material and relevant to their own research at their leisure.

Time outline

Activity Time
Accessing Human Cell Atlas data from Bioconductor 20m
Accessing CellxGene data from Bioconductor 15m
Bioconductor, AnVIL, and the HCA 7m

Learning goals

  • Explore Human Cell Atlas (HCA) data sets available through the hca and cellxgenedp packages.
  • Launch AnVIL project workspaces for processing HCA data.

Learning objectives

  • Download specific HCA and cellxgene data sets.
  • Import loom or h5ad format files into R / Bioconductor.
  • Perform initial steps, e.g., visualization, of scRNAseq data, in preparation for more extensive analysis using OSCA.

Additional resources

Presentations on similar material include

  • Accessing Human Cell Atlas Data with R / Bioconductor and the hca package, 2021-10-06 slides
  • R / Bioconductor for Analysis and Comprehension of the Human Cell Atlas, 2022-07-20 slides