xcmsVisGUI: interactive raw LC-MS viewer (Shiny)

A local desktop Shiny app for visualising raw LC-MS data (TIC/BPC, EICs, spectra, 2D/3D MS maps, DDA precursors). Launch with run_app().

Details

Import policy: every used function is declared with a per-function @importFrom so the code calls bare names. Two deliberate exceptions:

• shiny and bslib are imported whole (@import) — they are the UI framework used in essentially every function and have no conflicts with our other imports; enumerating them per function adds noise, not safety.

• the RforMassSpectrometry S4 stack (Spectra/xcms/MsExperiment/BiocParallel/ mzR) is called with ::. Those packages export many overlapping generics (rtime, intensity, mz, filterMsLevel, spectra, ...) and some collide with base (close, filter); :: keeps the intended method source explicit and dispatch unambiguous — the "unresolvable conflict" case. %>% (magrittr) and %||% (rlang) are imported here once as operators.

See also

Useful links:

• https://stanstrup.github.io/xcmsVisGUI

• https://github.com/stanstrup/xcmsVisGUI

• Report bugs at https://github.com/stanstrup/xcmsVisGUI/issues

Author

Maintainer: Jan Stanstrup stanstrup@gmail.com

Authors:

• Jan Stanstrup stanstrup@gmail.com