synapter: Label-free data analysis pipeline for optimal identification and quantitation

The synapter package provides functionality to reanalyse label-free proteomics data acquired on a Synapt G2 mass spectrometer. One or several runs, possibly processed with additional ion mobility separation to increase identification accuracy can be combined to other quantitation files to maximise identification and quantitation accuracy.

Author
Laurent Gatto, Nick J. Bond and Pavel V. Shliaha and Sebastian Gibb.
Date of publication
None
Maintainer
Laurent Gatto <lg390@cam.ac.uk> and Sebastian Gibb <mail@sebastiangibb.de>
License
GPL-2
Version
1.16.0
URLs

View on Bioconductor

Man pages

defunct
synapter Deprecated and Defunct
estimateMasterFdr
Computes FDR for all possible final peptide combinations
inspectPeptideScores
Inspect peptide scores.
makeMaster
Merges final peptide files
MasterFdrResults-class
Class '"MasterFdrResults"'
MasterPeptides-class
Class '"MasterPeptides"'
Synapter
Class "Synapter"
synapterGuide
Opens the 'synapter' vignette
synapter-package
Combine label-free data for optimal identification and...
synapterTinyData
Loads a small test data for the 'synapter' package
synergise
Synergise identification and quantitation results

Files in this package

synapter/DESCRIPTION
synapter/NAMESPACE
synapter/NEWS
synapter/R
synapter/R/AllClasses.R
synapter/R/AllGenerics.R
synapter/R/exported_tools.R
synapter/R/fasta.R
synapter/R/figures.R
synapter/R/gui.R
synapter/R/master.R
synapter/R/synapter-class.R
synapter/R/synapter-interface.R
synapter/R/synergise.R
synapter/R/utils.R
synapter/R/zzz.R
synapter/build
synapter/build/vignette.rds
synapter/data
synapter/data/synapterTiny.rda
synapter/inst
synapter/inst/CITATION
synapter/inst/doc
synapter/inst/doc/synapter.R
synapter/inst/doc/synapter.Rnw
synapter/inst/doc/synapter.pdf
synapter/inst/extdata
synapter/inst/extdata/04_test_database.fasta
synapter/inst/extdata/synapter.css
synapter/inst/scripts
synapter/inst/scripts/run_test_report.R
synapter/man
synapter/man/MasterFdrResults-class.Rd
synapter/man/MasterPeptides-class.Rd
synapter/man/Synapter.Rd
synapter/man/defunct.Rd
synapter/man/estimateMasterFdr.Rd
synapter/man/inspectPeptideScores.Rd
synapter/man/makeMaster.Rd
synapter/man/synapter-package.Rd
synapter/man/synapterGuide.Rd
synapter/man/synapterTinyData.Rd
synapter/man/synergise.Rd
synapter/vignettes
synapter/vignettes/Figures
synapter/vignettes/Figures/GUI-Tab1.jpg
synapter/vignettes/Figures/GUI-Tab2.jpg
synapter/vignettes/Figures/GUI-Tab3.jpg
synapter/vignettes/Figures/PLGS_create_databank1.jpg
synapter/vignettes/Figures/PLGS_create_databank2.jpg
synapter/vignettes/Figures/PLGS_db_search_options.jpg
synapter/vignettes/Figures/PLGS_output_files1.jpg
synapter/vignettes/Figures/PLGS_output_files2.jpg
synapter/vignettes/Figures/PLGS_output_files3.jpg
synapter/vignettes/synapter.Rnw
synapter/vignettes/synapter.bib