DOI: 10.18129/B9.bioc.HCAMatrixBrowser    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

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 <marcel.ramos at roswellpark.org>, Martin Morgan <mtmorgan.bioc at gmail.com>

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.


PDF   Reference Manual


biocViews DataRepresentation, Infrastructure, Software
Version 1.1.4
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
Suggests Me
Links To Me
Build Report  

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
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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