This Vignette goes over how to
launch the MSstatsShiny R shiny application.
To install this package, start R (version “4.0”) and enter:
MSstatsShiny is an R-shiny based GUI package integrated
with the MSstats family of packages. The package allows
users to analyze a variety of proteomic experiments, including those
processed using different labeling methods, spectral processing tools,
and targeting different biological questions of interest. It is designed
to enhance the usability of the MSstats packages, bringing
them to a wider user base, including those who do not have have
experience coding in R. The GUI is designed to be general, reproducible,
and scalable, as well as easily usable by all users. Finally, it
enhances both reproducibility and collaboration through documenting
analyses via code, which recreates the user’s analysis exactly.
After installation, running the application is as simple as executing a single command.
Once this command is executed, the application will automatically start up in a different window. You can still view any warnings or errors in the R console where you ran the function. This can be helpful when debugging.
MSstatsShiny is also available on the cloud at . Due to
RAM constraints, the cloud version of the application is limited to
files under 250 MB. Any larger files should be processed in a local
instance of the application.
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.4.2 (2024-10-31)
#> os Ubuntu 24.04.1 LTS
#> system x86_64, linux-gnu
#> ui X11
#> language (EN)
#> collate C
#> ctype en_US.UTF-8
#> tz Etc/UTC
#> date 2024-12-21
#> pandoc 3.2.1 @ /usr/local/bin/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> backports 1.5.0 2024-05-23 [2] RSPM (R 4.4.0)
#> base64enc 0.1-3 2015-07-28 [2] RSPM (R 4.4.0)
#> BiocGenerics 0.53.3 2024-12-15 [2] https://bioc.r-universe.dev (R 4.4.2)
#> Biostrings 2.75.3 2024-12-16 [2] https://bioc.r-universe.dev (R 4.4.2)
#> bitops 1.0-9 2024-10-03 [2] RSPM (R 4.4.0)
#> boot 1.3-31 2024-08-28 [2] RSPM (R 4.4.0)
#> brio 1.1.5 2024-04-24 [2] RSPM (R 4.4.0)
#> bslib 0.8.0 2024-07-29 [2] RSPM (R 4.4.0)
#> buildtools 1.0.0 2024-12-16 [3] local (/pkg)
#> cachem 1.1.0 2024-05-16 [2] RSPM (R 4.4.0)
#> caTools 1.18.3 2024-09-04 [2] RSPM (R 4.4.0)
#> cellranger 1.1.0 2016-07-27 [2] RSPM (R 4.4.0)
#> checkmate 2.3.2 2024-07-29 [2] RSPM (R 4.4.0)
#> cli 3.6.3 2024-06-21 [2] RSPM (R 4.4.0)
#> cluster 2.1.8 2024-12-11 [2] RSPM (R 4.4.0)
#> colorspace 2.1-1 2024-07-26 [2] RSPM (R 4.4.0)
#> crayon 1.5.3 2024-06-20 [2] RSPM (R 4.4.0)
#> data.table 1.16.4 2024-12-06 [2] RSPM (R 4.4.0)
#> digest 0.6.37 2024-08-19 [2] RSPM (R 4.4.0)
#> dplyr 1.1.4 2023-11-17 [2] RSPM (R 4.4.0)
#> DT 0.33 2024-04-04 [2] RSPM (R 4.4.0)
#> evaluate 1.0.1 2024-10-10 [2] RSPM (R 4.4.0)
#> fastmap 1.2.0 2024-05-15 [2] RSPM (R 4.4.0)
#> foreign 0.8-87 2024-06-26 [2] RSPM (R 4.4.0)
#> Formula 1.2-5 2023-02-24 [2] RSPM (R 4.4.0)
#> generics 0.1.3 2022-07-05 [2] RSPM (R 4.4.0)
#> GenomeInfoDb 1.43.2 2024-11-28 [2] https://bioc.r-universe.dev (R 4.4.2)
#> GenomeInfoDbData 1.2.13 2024-12-21 [2] Bioconductor
#> ggplot2 3.5.1 2024-04-23 [2] RSPM (R 4.4.0)
#> ggrepel 0.9.6 2024-09-07 [2] RSPM (R 4.4.0)
#> glue 1.8.0 2024-09-30 [2] RSPM (R 4.4.0)
#> gplots 3.2.0 2024-10-05 [2] RSPM (R 4.4.0)
#> gridExtra 2.3 2017-09-09 [2] RSPM (R 4.4.0)
#> gtable 0.3.6 2024-10-25 [2] RSPM (R 4.4.0)
#> gtools 3.9.5 2023-11-20 [2] RSPM (R 4.4.0)
#> Hmisc 5.2-1 2024-12-02 [2] RSPM (R 4.4.0)
#> htmlTable 2.4.3 2024-07-21 [2] RSPM (R 4.4.0)
#> htmltools 0.5.8.1 2024-04-04 [2] RSPM (R 4.4.0)
#> htmlwidgets 1.6.4 2023-12-06 [2] RSPM (R 4.4.0)
#> httpuv 1.6.15 2024-03-26 [2] RSPM (R 4.4.0)
#> httr 1.4.7 2023-08-15 [2] RSPM (R 4.4.0)
#> IRanges 2.41.2 2024-12-03 [2] https://bioc.r-universe.dev (R 4.4.2)
#> jquerylib 0.1.4 2021-04-26 [2] RSPM (R 4.4.0)
#> jsonlite 1.8.9 2024-09-20 [2] RSPM (R 4.4.0)
#> KernSmooth 2.23-24 2024-05-17 [2] RSPM (R 4.4.0)
#> knitr 1.49 2024-11-08 [2] RSPM (R 4.4.0)
#> later 1.4.1 2024-11-27 [2] RSPM (R 4.4.0)
#> lattice 0.22-6 2024-03-20 [2] RSPM (R 4.4.0)
#> lazyeval 0.2.2 2019-03-15 [2] RSPM (R 4.4.0)
#> lifecycle 1.0.4 2023-11-07 [2] RSPM (R 4.4.0)
#> limma 3.63.2 2024-12-11 [2] https://bioc.r-universe.dev (R 4.4.2)
#> lme4 1.1-35.5 2024-07-03 [2] RSPM (R 4.4.0)
#> lmerTest 3.1-3 2020-10-23 [2] RSPM (R 4.4.0)
#> log4r 0.4.4 2024-10-12 [2] RSPM (R 4.4.0)
#> magrittr 2.0.3 2022-03-30 [2] RSPM (R 4.4.0)
#> maketools 1.3.1 2024-10-04 [3] RSPM (R 4.4.0)
#> marray 1.85.0 2024-12-19 [2] https://bioc.r-universe.dev (R 4.4.2)
#> MASS 7.3-61 2024-06-13 [2] RSPM (R 4.4.0)
#> Matrix 1.7-1 2024-10-18 [2] RSPM (R 4.4.0)
#> mime 0.12 2021-09-28 [2] RSPM (R 4.4.0)
#> minqa 1.2.8 2024-08-17 [2] RSPM (R 4.4.0)
#> mockery 0.4.4 2023-09-26 [2] RSPM (R 4.4.0)
#> MSstats 4.15.0 2024-11-29 [2] https://bioc.r-universe.dev (R 4.4.2)
#> MSstatsConvert 1.17.0 2024-11-22 [2] https://bioc.r-universe.dev (R 4.4.2)
#> MSstatsPTM 2.9.1 2024-11-26 [2] https://bioc.r-universe.dev (R 4.4.2)
#> MSstatsShiny * 1.9.0 2024-12-21 [1] https://bioc.r-universe.dev (R 4.4.2)
#> MSstatsTMT 2.15.1 2024-12-18 [2] https://bioc.r-universe.dev (R 4.4.2)
#> munsell 0.5.1 2024-04-01 [2] RSPM (R 4.4.0)
#> nlme 3.1-166 2024-08-14 [2] RSPM (R 4.4.0)
#> nloptr 2.1.1 2024-06-25 [2] RSPM (R 4.4.0)
#> nnet 7.3-19 2023-05-03 [2] RSPM (R 4.4.0)
#> numDeriv 2016.8-1.1 2019-06-06 [2] RSPM (R 4.4.0)
#> pillar 1.10.0 2024-12-17 [2] RSPM (R 4.4.0)
#> pkgconfig 2.0.3 2019-09-22 [2] RSPM (R 4.4.0)
#> plotly 4.10.4 2024-01-13 [2] RSPM (R 4.4.0)
#> preprocessCore 1.69.0 2024-11-30 [2] https://bioc.r-universe.dev (R 4.4.2)
#> promises 1.3.2 2024-11-28 [2] RSPM (R 4.4.0)
#> purrr 1.0.2 2023-08-10 [2] RSPM (R 4.4.0)
#> R6 2.5.1 2021-08-19 [2] RSPM (R 4.4.0)
#> Rcpp 1.0.13-1 2024-11-02 [2] RSPM (R 4.4.0)
#> readxl 1.4.3 2023-07-06 [2] RSPM (R 4.4.0)
#> rlang 1.1.4 2024-06-04 [2] RSPM (R 4.4.0)
#> rmarkdown * 2.29 2024-11-04 [2] RSPM (R 4.4.0)
#> rpart 4.1.23 2023-12-05 [2] RSPM (R 4.4.0)
#> rstudioapi 0.17.1 2024-10-22 [2] RSPM (R 4.4.0)
#> S4Vectors 0.45.2 2024-12-16 [2] https://bioc.r-universe.dev (R 4.4.2)
#> sass 0.4.9 2024-03-15 [2] RSPM (R 4.4.0)
#> scales 1.3.0 2023-11-28 [2] RSPM (R 4.4.0)
#> sessioninfo 1.2.2 2021-12-06 [2] RSPM (R 4.4.0)
#> shiny 1.10.0 2024-12-14 [2] RSPM (R 4.4.0)
#> shinyBS 0.61.1 2022-04-17 [2] RSPM (R 4.4.0)
#> shinybusy 0.3.3 2024-03-09 [2] RSPM (R 4.4.0)
#> shinyjs 2.1.0 2021-12-23 [2] RSPM (R 4.4.0)
#> statmod 1.5.0 2023-01-06 [2] RSPM (R 4.4.0)
#> stringi 1.8.4 2024-05-06 [2] RSPM (R 4.4.0)
#> stringr 1.5.1 2023-11-14 [2] RSPM (R 4.4.0)
#> survival 3.8-3 2024-12-17 [2] RSPM (R 4.4.0)
#> sys 3.4.3 2024-10-04 [2] RSPM (R 4.4.0)
#> testthat 3.2.2 2024-12-10 [2] RSPM (R 4.4.0)
#> tibble 3.2.1 2023-03-20 [2] RSPM (R 4.4.0)
#> tidyr 1.3.1 2024-01-24 [2] RSPM (R 4.4.0)
#> tidyselect 1.2.1 2024-03-11 [2] RSPM (R 4.4.0)
#> UCSC.utils 1.3.0 2024-11-30 [2] https://bioc.r-universe.dev (R 4.4.2)
#> uuid 1.2-1 2024-07-29 [2] RSPM (R 4.4.0)
#> vctrs 0.6.5 2023-12-01 [2] RSPM (R 4.4.0)
#> viridisLite 0.4.2 2023-05-02 [2] RSPM (R 4.4.0)
#> xfun 0.49 2024-10-31 [2] RSPM (R 4.4.0)
#> xtable 1.8-4 2019-04-21 [2] RSPM (R 4.4.0)
#> XVector 0.47.1 2024-12-20 [2] https://bioc.r-universe.dev (R 4.4.2)
#> yaml 2.3.10 2024-07-26 [2] RSPM (R 4.4.0)
#>
#> [1] /tmp/RtmpTsRaky/Rinst197778ba16ff
#> [2] /github/workspace/pkglib
#> [3] /usr/local/lib/R/site-library
#> [4] /usr/lib/R/site-library
#> [5] /usr/lib/R/library
#>
#> ──────────────────────────────────────────────────────────────────────────────