ImmuneSpaceR

DOI: 10.18129/B9.bioc.ImmuneSpaceR    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ImmuneSpaceR.

A Thin Wrapper around the ImmuneSpace Database

Bioconductor version: 3.9

Provides a convenient API for accessing data sets within ImmuneSpace (www.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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

HTML	R Script	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
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, DataRepresentation, Software, ThirdPartyClient
Version	1.12.2
In Bioconductor since	BioC 3.3 (R-3.3) (3.5 years)
License	GPL-2
Depends
Imports	utils, R6, data.table, curl, httr, Rlabkey (>= 2.1.136), Biobase, pheatmap, ggplot2 (>= 3.2.0), scales, stats, gplots, plotly, heatmaply (>= 0.7.0), jsonlite, rmarkdown, preprocessCore, flowCore, flowWorkspace, digest
LinkingTo
Suggests	knitr, testthat
SystemRequirements
Enhances
URL	https://github.com/RGLab/ImmuneSpaceR
BugReports	https://github.com/RGLab/ImmuneSpaceR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	ImmuneSpaceR_1.12.2.tar.gz
Windows Binary	ImmuneSpaceR_1.12.2.zip
Mac OS X 10.11 (El Capitan)	ImmuneSpaceR_1.12.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ImmuneSpaceR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ImmuneSpaceR
Package Short Url	https://bioconductor.org/packages/ImmuneSpaceR/
Package Downloads Report	Download Stats