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README.md
# ImmuneSpaceR <img src="man/figures/logo.png" align="right" /> <!-- badges: start --> [![R build status](https://github.com/RGLab/ImmuneSpaceR/workflows/R-CMD-check/badge.svg)](https://github.com/RGLab/ImmuneSpaceR/actions) [![Codecov test coverage](https://codecov.io/gh/RGLab/ImmuneSpaceR/branch/main/graph/badge.svg)](https://codecov.io/gh/RGLab/ImmuneSpaceR?branch=main) [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable) [![Years in BioC](http://www.bioconductor.org/shields/years-in-bioc/ImmuneSpaceR.svg)](http://bioconductor.org/packages/release/bioc/html/ImmuneSpaceR.html) [![BioC status](http://www.bioconductor.org/shields/build/release/bioc/ImmuneSpaceR.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/ImmuneSpaceR) [![Downloads](http://www.bioconductor.org/shields/downloads/ImmuneSpaceR.svg)](https://bioconductor.org/packages/stats/bioc/ImmuneSpaceR/) [![Updated](https://bioconductor.org/shields/lastcommit/release/bioc/ImmuneSpaceR.svg)](http://bioconductor.org/packages/release/bioc/news/ImmuneSpaceR/NEWS) <!-- badges: end --> > Please update the URL (machine name) to `datatools.immunespace.org` from `www.immunespace.org` in your `.netrc` file. A thin wrapper around Rlabkey to access the [ImmuneSpace Data & Tools Portal](https://datatools.immunespace.org) from R. This package simplifies access to the [HIPC](https://www.immuneprofiling.org/) ImmuneSpace database for R programmers. It takes advantage of the standardization of the database to hide all the [`Rlabkey`](https://cran.r-project.org/web/packages/Rlabkey/index.html) specific code away from the user. The study-specific datasets can be accessed via an object-oriented paradigm. ## Installation Install from [Bioconductor](http://bioconductor.org/packages/release/bioc/html/ImmuneSpaceR.html): ``` r install.packages("BiocManager") BiocManager::install("ImmuneSpaceR") ``` Or install the latest development version via [`remotes`](https://cran.r-project.org/web/packages/remotes/index.html): ``` 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](https://datatools.immunespace.org/login/home/register.view?) 1. 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](https://rglab.github.io/ImmuneSpaceR/articles/Intro_to_ImmuneSpaceR.html). ## 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$listDatasets() ``` which will print names of available datasets and gene expression matrices. ### Retrieve datasets Gene expression matrices or datasets can be retreived by: ``` r LAIV2008 <- con$getGEMatrix("SDY269_PBMC_LAIV_Geo") elisa <- con$getDataset("elisa") ``` The connection object *caches* data, so once it is retrieved, the next time you access it, it will use the local cached copy. The package uses a [R6](https://cran.r-project.org/web/packages/R6/index.html) class system to represent the connection to a study and get around some of R's copy-on-change behaviour. ### Visualize The `plot` method uses [`ggplot2`](https://cran.r-project.org/web/packages/ggplot2/index.html) functions to generate visualizations of datasets, leveraging the standardized dataset tables. ``` r con$plot("hai") ``` ## Examples & Documentation For more advanced examples and detailed documentation, see [the package vignettes](http://rglab.github.io/ImmuneSpaceR/articles/) and the reports available on [ImmuneSpace](https://datatools.immunespace.org/). ## Contributing If you'd like to report bugs/issues/feature requests or contribute to the package, please see [the contributing guidelines](./CONTRIBUTING.md) and join [our Slack workspace](https://immunespace.herokuapp.com/).