DOI: 10.18129/B9.bioc.HCAMatrixBrowser    

This is the development version of HCAMatrixBrowser; for the stable release version, see HCAMatrixBrowser.

Extract and manage matrix data from the Human Cell Atlas project

Bioconductor version: Development (3.13)

The HCAMatrixBrowser queries the HCA matrix endpoint to download expression data and returns a standard Bioconductor object. It uses the LoomExperiment package to serve matrix data that is downloaded as HDF5 loom format.

Author: Marcel Ramos [aut, cre] , Martin Morgan [aut] (0000-002-5874-8148)

Maintainer: Marcel Ramos <marcel.ramos at roswellpark.org>

Citation (from within R, enter citation("HCAMatrixBrowser")):


To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script HCAMatrix API Queries
HTML R Script HCAMatrixBrowser Quick Start
PDF   Reference Manual
Text   NEWS


biocViews DataRepresentation, Infrastructure, Software
Version 1.1.3
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
License Artistic-2.0
Depends R (>= 4.0.0), AnVIL
Imports BiocFileCache, digest, dplyr, httr, jsonlite, Matrix, methods, progress, rlang, SingleCellExperiment, stats, utils
Suggests BiocStyle, knitr, HCABrowser, LoomExperiment(>= 1.5.3), readr
BugReports https://github.com/Bioconductor/HCAMatrixBrowser
Depends On Me
Imports Me HCAExplorer, SingleCellMultiModal
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package HCAMatrixBrowser_1.1.3.tar.gz
Windows Binary HCAMatrixBrowser_1.1.3.zip (32- & 64-bit)
macOS 10.13 (High Sierra) HCAMatrixBrowser_1.1.3.tgz
Source Repository git clone https://git.bioconductor.org/packages/HCAMatrixBrowser
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HCAMatrixBrowser
Package Short Url https://bioconductor.org/packages/HCAMatrixBrowser/
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