ImmuneSpaceR

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see ImmuneSpaceR.

A Thin Wrapper around the ImmuneSpace Data and Tools Portal

Bioconductor version: 3.17

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, DataRepresentation, Software, ThirdPartyClient

Version 1.28.0

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

Suggests knitr, testthat, covr, withr

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