DOI: 10.18129/B9.bioc.HCAMatrixBrowser    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see HCAMatrixBrowser.

Extract and manage matrix data from the Human Cell Atlas project

Bioconductor version: 3.12

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 "4.0") and enter:

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


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 1.0.1
In Bioconductor since BioC 3.12 (R-4.0) (0.5 years)
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_1.0.1.tar.gz
Windows Binary HCAMatrixBrowser_1.0.1.zip
macOS 10.13 (High Sierra) HCAMatrixBrowser_1.0.1.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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