HCAMatrixBrowser

This package is for version 3.12 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see HCAMatrixBrowser.

Extract and manage matrix data from the Human Cell Atlas project

DOI: 10.18129/B9.bioc.HCAMatrixBrowser

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")):

Installation

To install this package, start R (version "4.0") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("HCAMatrixBrowser")

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

Documentation

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

browseVignettes("HCAMatrixBrowser")

HCAMatrix API Queries HTML R Script

HCAMatrixBrowser Quick Start HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataRepresentation, Infrastructure, Software

Version 1.0.1

In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)

License Artistic-2.0

Depends R (>= 4.0.0), AnVIL

Imports BiocFileCache, digest, dplyr, httr, jsonlite, Matrix, methods, progress, rlang, SingleCellExperiment, stats, utils

System Requirements

URL

Bug Reports https://github.com/Bioconductor/HCAMatrixBrowser

Suggests BiocStyle, knitr, HCABrowser, LoomExperiment(>= 1.5.3), readr

Linking To

Enhances

Depends On Me

Imports Me HCAExplorer, SingleCellMultiModal

Suggests Me

Links To Me

Build Report 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

Bioc Package Browser https://code.bioconductor.org/browse/HCAMatrixBrowser/

Package Short Url https://bioconductor.org/packages/HCAMatrixBrowser/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.12 Source Archive