by John D. Gagnon
University of California, San Francisco
Overview
Installation
Usage
Session info
License
A shinyapp-based GUI to identify available antibodies
- If you do not already have R installed, or your version is out of date, download and install the latest version.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.
- Download the package from GitHub
install.packages("devtools")
devtools::install_github("jdgagnon/antibodySeek")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()
- 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
csvfile
OR
-
Load a spreadsheet from
Google Sheetsby filling out the spreadsheet name and clickingFind Google Sheet. -
Choose the approprate worksheet
- Select the antibodies from the dropdown menu that you wish to use.
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