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ImmuneSpaceR

A Thin Wrapper around the ImmuneSpace Data and Tools Portal


Bioconductor version: Release (3.18)

Provides a convenient API for accessing data sets within ImmuneSpace Data and Tools Portal (datatools.immunespace.org), the data repository and analysis platform of the Human Immunology Project Consortium (HIPC).

Author: Greg Finak [aut], Renan Sauteraud [aut], Mike Jiang [aut], Gil Guday [aut], Leo Dashevskiy [aut], Evan Henrich [aut], Ju Yeong Kim [aut], Lauren Wolfe [aut], Helen Miller [aut], Raphael Gottardo [aut], ImmuneSpace Package Maintainer [cre, cph]

Maintainer: ImmuneSpace Package Maintainer <immunespace at gmail.com>

Citation (from within R, enter citation("ImmuneSpaceR")):

Installation

To install this package, start R (version "4.3") and enter:


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

BiocManager::install("ImmuneSpaceR")

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("ImmuneSpaceR")
An Introduction to the ImmuneSpaceR Package HTML R Script
Downloading Datasets with getDataset HTML R Script
Handling Expression Matrices with ImmuneSpaceR HTML R Script
interactive_netrc() Function Walkthrough HTML R Script
SDY144: Correlation of HAI/Virus Neutralizition Titer and Cell Counts HTML R Script
SDY180: Abundance of Plasmablasts Measured by Multiparameter Flow Cytometry HTML R Script
SDY269: Correlating HAI with Flow Cytometry and ELISPOT Results HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, DataRepresentation, Software, ThirdPartyClient
Version 1.30.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL-2
Depends R (>= 3.5.0)
Imports utils, R6, data.table, curl, httr, Rlabkey (>= 2.3.1), Biobase, pheatmap, ggplot2 (>= 3.2.0), scales, stats, gplots, plotly, heatmaply (>= 0.7.0), jsonlite, rmarkdown, preprocessCore, flowCore, flowWorkspace, digest
System Requirements
URL https://github.com/RGLab/ImmuneSpaceR
Bug Reports https://github.com/RGLab/ImmuneSpaceR/issues
See More
Suggests knitr, testthat, covr, withr
Linking To
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Depends On Me
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Build Report Build Report

Package Archives

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

Source Package ImmuneSpaceR_1.30.0.tar.gz
Windows Binary ImmuneSpaceR_1.30.0.zip (64-bit only)
macOS Binary (x86_64) ImmuneSpaceR_1.30.0.tgz
macOS Binary (arm64) ImmuneSpaceR_1.30.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ImmuneSpaceR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ImmuneSpaceR
Bioc Package Browser https://code.bioconductor.org/browse/ImmuneSpaceR/
Package Short Url https://bioconductor.org/packages/ImmuneSpaceR/
Package Downloads Report Download Stats