README.md

In jdgagnon/antibodySeek: Create a table of antibodies available.

antibodySeek

by John D. Gagnon University of California, San Francisco

Table of Contents

Overview Installation Usage Session info License

Overview

A shinyapp-based GUI to identify available antibodies

Installation

1. If you do not already have R installed, or your version is out of date, download and install the latest version.

• Optionally, install the latest version of RStudio Desktop.

1. Download the package from GitHub

install.packages("devtools")
devtools::install_github("jdgagnon/antibodySeek")

Usage

Load the package into the R session.

library(antibodySeek)

To initialize the shiny app, paste the following code in your R console and run it.

antibodySeek()

1. Load a spreadsheet containing the antibody database:

• Spreadsheet must be in the following format:

| Antibody | PE | FITC | etc… | | :------- | :- | :--- | :--- | | CD3 | X | | | | CD4 | | X | X | | CD8 | X | X | X |

• Use the file browser to select a csv file

OR

• Load a spreadsheet from Google Sheets by filling out the spreadsheet name and clicking Find Google Sheet.

• Choose the approprate worksheet

1. Select the antibodies from the dropdown menu that you wish to use.

Session info

Here is the output of sessionInfo() on the system on which this package was developed:

sessionInfo()
#> R version 3.5.1 (2018-07-02)
#> Platform: x86_64-apple-darwin17.6.0 (64-bit)
#> Running under: macOS High Sierra 10.13.6
#> 
#> Matrix products: default
#> BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
#> LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
#> 
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] compiler_3.5.1  backports_1.1.2 magrittr_1.5    rprojroot_1.3-2
#>  [5] tools_3.5.1     htmltools_0.3.6 yaml_2.2.0      Rcpp_0.12.18   
#>  [9] stringi_1.2.4   rmarkdown_1.10  highr_0.7       knitr_1.20     
#> [13] stringr_1.3.1   digest_0.6.17   evaluate_0.11

License

GNU GPL-3.0-or-later

jdgagnon/antibodySeek documentation built on May 17, 2019, 12:02 p.m.