HCAMatrixBrowser

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")):

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("HCAMatrixBrowser")

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

Documentation

PDF   Reference Manual

Details

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
LinkingTo
Suggests BiocStyle, knitr, HCABrowser, LoomExperiment(>= 1.5.3), readr
SystemRequirements
Enhances
URL
BugReports https://github.com/Bioconductor/HCAMatrixBrowser
Depends On Me
Imports Me HCAExplorer
Suggests Me
Links To Me
Build Report  

Package Archives

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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