Code associated with the R Shiny App CYANUS.
Code required for the paper "Systematic Evaluation of Existing and Novel Approaches for Differential Expression Anaylsis on Real and Simulated CyTOF Data" can now be found at biomedbigdata/Cyanus-Paper-Code.
User-friendly R Shiny App Analyzing Cytometry Data
The public web interface is available at https://exbio.wzw.tum.de/cyanus/.
The source code can be found in ui/, server/, functions/, server.R and ui.R.
Additionally, a docker image for our shiny app is publicly available on Docker Hub. First, make sure docker is installed on your machine. Then run
docker pull quirinmanz/cyanus:latestYou can run the app in a single container using
docker run --rm -p 3838:3838 quirinmanz/cyanus:latestIf you go to localhost:3838, you can see our Shiny app.
You can also run the Shiny App in your R session with shiny::runApp().
In that case, you have to restore the project library using
renv:
# install.packages('renv')
renv::restore()To use multiple instances of the app, we configured nginx and shinyproxy with docker. The command to use this production-ready version of CYANUS is
docker-compose up -dLis Arend, Judith Bernett, Quirin Manz, Melissa Klug, Olga Lazareva, Jan Baumbach, Dario Bongiovanni, Markus List, A systematic comparison of novel and existing differential analysis methods for CyTOF data, Briefings in Bioinformatics, 2021;, bbab471, https://doi.org/10.1093/bib/bbab471
If you have difficulties using CYANUS, please open an issue. If issues on the simulation of data or evaluation of methods arise, you can either open an issue or contact the authors of the paper.
| Package | License |
|---|---|
| CATALYST | GPL (>=2) |
| HDCytoData | MIT + file LICENSE |
| readxl | GPL-3 |
| data.table | MPL-2.0 | file LICENSE |
| ggplot2 | MIT + file LICENSE |
| BiocParallel | GPL-2 | GPL-3 |
| fs | GPL-3 |
| SummarizedExperiment | Artistic-2.0 |
| dplyr | MIT + file LICENSE |
| reshape2 | MIT + file LICENSE |
| ggside | MIT + file LICENSE |
| cowplot | GPL-2 |
| ggpubr | GPL-2 |
| ComplexHeatmap | MIT + file LICENSE |
| ConsensusClusterPlus | GPL version 2 |
| flowCore | Artistic-2.0 |
| FlowSOM | GPL (>= 2) |
| ggridges | GPL-2 | file LICENSE |
| graphics | Part of R 4.0.5 |
| grDevices | Part of R 4.0.5 |
| grid | Part of R 4.0.5 |
| igraph | GPL (>= 2) |
| purrr | GPL-3 | file LICENSE |
| RColorBrewer | Apache License 2.0 |
| S4Vectors | Artistic-2.0 |
| Rcpp | GPL (>= 2) |
| RcppAlgos | GPL (>= 2) |
| CytoGLMM | LGPL-3 |
| MASS | GPL-2 | GPL-3 |
| diffcyt | MIT + file LICENSE |
| rstatix | GPL-2 |
| multcomp | GPL-2 |
| gamlss | GPL-2 | GPL-3 |
| gamlss.dist | GPL-2 | GPL-3 |
| lme4 | GPL (>= 2) |
| circlize | MIT + file LICENSE |
| magrittr | MIT + file LICENSE |
| scales | MIT + file LICENSE |
| dimRed | GPL-3 | file LICENSE |
| ggvenn | MIT + file LICENSE |
| RANN | GPL (>= 3) |
| uwot | GPL (>= 3) |
| renv | MIT + file LICENSE |
| shinydashboard | GPL (>= 2) | file LICENSE |
| shinyjs | MIT + file LICENSE |
| shinyWidgets | GPL-3 |
| stats | Part of R 4.0.5 |
| DT | GPL-3 | file LICENSE |
| shiny | GPL-3 | file LICENSE |
| shinycssloaders | MIT + file LICENSE |
| shinyBS | GPL-3 |
| sortable | MIT + file LICENSE |
| xlsx | GPL-3 |
| plotly | MIT + file LICENSE |
| waiter | MIT + file LICENSE |