This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see 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")
):
To install this package, start R (version "4.0") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("HCAMatrixBrowser")
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:
browseVignettes("HCAMatrixBrowser")
HTML | R Script | HCAMatrix API Queries |
HTML | R Script | HCAMatrixBrowser Quick Start |
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 |
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, SingleCellMultiModal |
Suggests Me | |
Links To Me | |
Build Report |
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/ |
Package Downloads Report | Download Stats |
Documentation »
Bioconductor
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations: