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<!-- is generated from README.Rmd. Please edit that file --> ImmuneSpaceR <img src="man/figures/logo.png" align="right" /> ============================================================= [![Build Status](]( [![codecov](]( [![bioc](]( [![bioc](]( A thin wrapper around Rlabkey to access the [ImmuneSpace]( database from R. This package simplifies access to the [HIPC]( ImmuneSpace database for R programmers. It takes advantage of the standardization of the database to hide all the [`Rlabkey`]( specific code away from the user. The study-specific datasets can be accessed via an object-oriented paradigm. Installation ------------ Install from [Bioconductor]( ``` r install.packages("BiocManager") BiocManager::install("ImmuneSpaceR") ``` Or install the latest development version via [`remotes`]( ``` r install.packages("remotes") remotes::install_github("RGLab/ImmuneSpaceR") ``` Configuration ------------- The ImmuneSpace Portal can be accessed via `ImmuneSpaceR` with the user's credentials. A `.netrc` file storing login and password information is required. 1. [Register]( 2. Create a netrc file with your ImmuneSpace credetntials using `interactive_netrc()` function in R: ``` r library(ImmuneSpaceR) interactive_netrc() ``` If you're familiar with the command-line interface, see [the introductory vignette]( Usage ----- ### Create a connection The general idea is that the user creates an instance of an `ImmuneSpaceConnection` class. The instance configures itself to connect to a specific study, and datasets and gene expression matrices can be retrieved by name. For example: ``` r library(ImmuneSpaceR) con <- CreateConnection("SDY269") ``` will create an instance of SDY269. ### List datasets Datasets can be listed by: ``` r con$listDatasets() #> datasets #> gene_expression_files #> fcs_sample_files #> demographics #> elispot #> hai #> elisa #> pcr #> cohort_membership #> fcs_analyzed_result #> Expression Matrices #> SDY269_PBMC_TIV_Geo #> SDY269_PBMC_LAIV_Geo ``` which will print names of available datasets and gene expression matrices. ### Retrieve datasets Gene expression matrices or datasets can be retreived by: ``` r LAIV2008 <- con$getGEMatrix("SDY269_PBMC_LAIV_Geo") #> Downloading matrix.. #> Constructing ExpressionSet elisa <- con$getDataset("elisa") ``` The connection object *caches* data, so once it is retrieved, the next time you access it, it will use the local cached copy. The package uses a [R6]( class system to represent the connection to a study and get around some of R's copy-on-change behaviour. ### Visualize The `plot` method uses [`ggplot2`]( functions to generate visualizations of datasets, leveraging the standardized dataset tables. ``` r con$plot("hai") ``` <img src="man/figures/README-plot-1.png" width="100%" /> Examples & Documentation ------------------------ For more advanced examples and detailed documentation, see [the package vignettes]( and the reports available on [ImmuneSpace]( Contributing ------------ If you'd like to report bugs/issues/feature requests or contribute to the package, please see [the contributing guidelines](./ and join [our Slack workspace](