| MSstatsShiny-package | MSstatsShiny: An R-shiny based package for detecting differencially abundant proteins, integrated with the MSstats family of packages. |
| annotation.mine | Example annotation file for Spectromine |
| annotation.mq | Example annotation file for MaxQuant |
| annotation.pd | Example annotation file for PD |
| apply_adj | Main PTM adjustment function |
| 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 |
| expdesServer | Expdes Server module for future experiments |
| expdesUI | Expdes UI module for future experiments UI. |
| groupComparisonPlots2 | Plotting funcitonality for QC plots |
| helpUI | Help UI module for help page. |
| homeUI | Home UI module for home page. |
| launch_MSstatsShiny | Run MSstatsShiny Application |
| lf_model | Main LF modeling function for MSstatsShiny application |
| lf_summarization_loop | Main LF calculation summarization function for MSstatsShiny application |
| loadpageServer | Loadpage Server module for data selection and upload server. |
| loadpageUI | Loadpage UI module for data selection and upload UI. |
| msstatsHelpUI | Help MSStats UI module for msstats help page. |
| MSstatsShiny | MSstatsShiny: An R-shiny based package for detecting differencially abundant proteins, integrated with the MSstats family of packages. |
| msstatsTmtHelpUI | Help MSStats UI module for msstatstmt help page. |
| proteinGroups | Example ProteinGroups file for MaxQuant |
| qcServer | QC Server module for data processing |
| qcUI | QC UI module for data processing UI. |
| QC_check | Quick QC value check |
| radioTooltip | Custom function to create radio tool tips |
| raw.mine | Example output file Spectromine |
| raw.om | Example output file Spectromine |
| raw.pd | Example output file PD |
| server | Server function for the MSstatsShiny app |
| statmodelServer | Statmodel Server module for stat inference |
| statmodelUI | Statmodel UI module for statistical inference UI. |
| tmt_model | Main TMT modeling function for MSstatsShiny application |
| tmt_pd_model | Example of TMT dataset modeled using MSstatsTMT 'groupComparisonTMT' function. |
| tmt_pd_summarized | Example of TMT dataset processed using MSstatsTMT summarization function. |
| tmt_summarization_loop | Main TMT summarization calculation function for MSstatsShiny application |
| uiObject | UI function for the MSstatsShiny app |
| xy_str | Simple function to return coordinates |