Package: MSstatsShiny 1.15.1

Anthony Wu

MSstatsShiny: MSstats GUI for Statistical Anaylsis of Proteomics Experiments

MSstatsShiny is an R-Shiny graphical user interface (GUI) integrated with the R packages MSstats, MSstatsTMT, and MSstatsPTM. It provides a point and click end-to-end analysis pipeline applicable to a wide variety of experimental designs. These include data-dependedent acquisitions (DDA) which are label-free or tandem mass tag (TMT)-based, as well as DIA, SRM, and PRM acquisitions and those targeting post-translational modifications (PTMs). The application automatically saves users selections and builds an R script that recreates their analysis, supporting reproducible data analysis.

Authors:Devon Kohler [aut], Anthony Wu [aut, cre], Deril Raju [aut], Maanasa Kaza [aut], Cristina Pasi [aut], Ting Huang [aut], Mateusz Staniak [aut], Dhaval Mohandas [aut], Eduard Sabido [aut], Meena Choi [aut], Olga Vitek [aut]

MSstatsShiny_1.15.1.tar.gz
MSstatsShiny_1.15.1.zip(r-4.7)MSstatsShiny_1.15.1.zip(r-4.6)MSstatsShiny_1.13.4.zip(r-4.5)
MSstatsShiny_1.15.1.tgz(r-4.6-any)MSstatsShiny_1.13.4.tgz(r-4.5-any)
MSstatsShiny_1.15.1.tar.gz(r-4.7-any)MSstatsShiny_1.15.1.tar.gz(r-4.6-any)
MSstatsShiny_1.15.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
MSstatsShiny/json (API)

# Install 'MSstatsShiny' in R:

install.packages('MSstatsShiny', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/vitek-lab/msstatsshiny/issues

Datasets:

annotation.mine - Example annotation file for Spectromine
annotation.mq - Example annotation file for MaxQuant
annotation.pd - Example annotation file for PD
dia_skyline_model - Example of Sklyine DDA dataset modeled using MSstats 'groupComparison' function.
dia_skyline_summarized - Example of Sklyine DDA dataset processed using MSstats summarization function.
evidence - Example evidence file for MaxQuant
example_dia_skyline - Example of input Sklyine DDA dataset.
example_skyline_annotation - Example annotation file
proteinGroups - Example ProteinGroups file for MaxQuant
raw.mine - Example output file Spectromine
raw.om - Example output file Spectromine
raw.pd - Example output file PD
tmt_pd_model - Example of TMT dataset modeled using MSstatsTMT 'groupComparisonTMT' function.
tmt_pd_summarized - Example of TMT dataset processed using MSstatsTMT summarization function.

On BioConductor:MSstatsShiny-1.15.1(bioc 3.24)MSstatsShiny-1.14.0(bioc 3.23)

immunooncology massspectrometry proteomics software shinyapps differentialexpression onechannel twochannel normalization qualitycontrol gui

7.52 score 20 stars 7 scripts 25 exports 183 dependencies

Last updated from:7d6bc41082. Checks:1 ERROR, 5 WARNING, 2 OK, 2 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	229
linux-devel-x86_64	WARNING	425
source / vignettes	OK	316
linux-release-x86_64	WARNING	409
macos-release-arm64	WARNING	363
macos-oldrel-arm64	FAIL	79
windows-devel	WARNING	343
windows-release	WARNING	307
windows-oldrel	FAIL	96
wasm-release	OK	235

Exports:apply_adj expdesServer expdesUI groupComparisonPlots2 helpUI homeUI launch_MSstatsShiny lf_model lf_summarization_loop loadpageServer loadpageUI msstatsHelpUI msstatsTmtHelpUI networkUI QC_check qcServer qcUI radioTooltip server statmodelServer statmodelUI tmt_model tmt_summarization_loop uiObject xy_str

Dependencies:arrow askpass assertthat backports base64enc BH BiocGenerics BiocParallel Biostrings bit bit64 bitops blob boot brio bslib cachem callr caTools cellranger checkmate cli clipr cluster codetools colorspace commonmark config cpp11 crayon crosstalk curl data.table DBI dbplyr desc diffobj digest dplyr DT evaluate farver fastmap float fontawesome foreign formatR Formula fs futile.logger futile.options generics ggplot2 ggrepel globals glue gplots gridExtra gtable gtools highr Hmisc hms htmlTable htmltools htmlwidgets httpuv httr IRanges isoband ISOcodes jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lazyeval lgr lifecycle limma lme4 lmerTest log4r magrittr marray MASS Matrix MatrixExtra memoise mime minqa mlapi mockery MSstats MSstatsBig MSstatsBioNet MSstatsConvert MSstatsPTM MSstatsResponse MSstatsTMT nlme nloptr nnet numDeriv openssl otel pillar pkgbuild pkgconfig pkgload plotly praise preprocessCore prettyunits processx progress promises ps purrr r2r R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack readr readxl reformulas rematch rentrez RhpcBLASctl rlang rmarkdown rpart rprojroot rsparse rstudioapi S4Vectors S7 sass scales Seqinfo shiny shinyBS shinybusy shinydashboard shinyFiles shinyjs snow sourcetools sparklyr statmod stopwords stringi stringr survival sys testthat text2vec tibble tidyr tidyselect tinytex tzdb utf8 uuid vctrs viridisLite vroom waldo withr xfun XML xml2 xtable XVector yaml

MSstatsShiny Launch Instructions

Installation | 1. Introduction | 2. Launch Function | 3. Cloud Version | 4. Session Info

Rendered fromMSstatsShiny_Launch_Instructions.Rmdusingknitr::rmarkdown

Last update: 2023-04-21
Started: 2022-09-26

Help page	Topics
Example annotation file for Spectromine	annotation.mine
Example annotation file for MaxQuant	annotation.mq
Example annotation file for PD	annotation.pd
Main PTM adjustment function	apply_adj
Example of Sklyine DDA dataset modeled using MSstats 'groupComparison' function.	dia_skyline_model
Example of Sklyine DDA dataset processed using MSstats summarization function.	dia_skyline_summarized
Example evidence file for MaxQuant	evidence
Example of input Sklyine DDA dataset.	example_dia_skyline
Example annotation file	example_skyline_annotation
Expdes Server module for future experiments	expdesServer
Expdes UI module for future experiments UI.	expdesUI
Get filename for plot download based on plot type	get_download_plot_filename
Plotting funcitonality for QC plots	groupComparisonPlots2
Help UI module for help page.	helpUI
Home UI module for home page.	homeUI
Run MSstatsShiny Application	launch_MSstatsShiny
Main LF modeling function for MSstatsShiny application	lf_model
Main LF calculation summarization function for MSstatsShiny application	lf_summarization_loop
Loadpage Server module for data selection and upload server.	loadpageServer
Loadpage UI module for data selection and upload UI.	loadpageUI
Help MSStats UI module for msstats help page.	msstatsHelpUI
Help MSStats UI module for msstatstmt help page.	msstatsTmtHelpUI
Network UI module for visualizing protein regulatory networks from INDRA.	networkUI
Example ProteinGroups file for MaxQuant	proteinGroups
Quick QC value check	QC_check
QC Server module for data processing	qcServer
QC UI module for data processing UI.	qcUI
Custom function to create radio tool tips	radioTooltip
Example output file Spectromine	raw.mine
Example output file Spectromine	raw.om
Example output file PD	raw.pd
Server function for the MSstatsShiny app	server
Statmodel Server module for stat inference	statmodelServer
Statmodel UI module for statistical inference UI.	statmodelUI
Main TMT modeling function for MSstatsShiny application	tmt_model
Example of TMT dataset modeled using MSstatsTMT 'groupComparisonTMT' function.	tmt_pd_model
Example of TMT dataset processed using MSstatsTMT summarization function.	tmt_pd_summarized
Main TMT summarization calculation function for MSstatsShiny application	tmt_summarization_loop
UI function for the MSstatsShiny app	uiObject
Server logic for network visualization module	visualizeNetworkServer
Simple function to return coordinates	xy_str
Zip PDF files and copy to download destination	zip_and_copy_plot

Package: MSstatsShiny 1.15.1

MSstatsShiny: MSstats GUI for Statistical Anaylsis of Proteomics Experiments

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