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
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("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 | ||
| NEWS | Text |
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 |
See More
| 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 |