This R package implements statistical modelling of affinity purification–mass spectrometry (AP-MS) data to compute confidence scores to identify bona fide protein-protein interactions (PPI).
Installation The development version can be installed through github:
devtools::install_github(repo="zqzneptune/SMAD") library(SMAD) Input Data A demo data.frame was provided as a hint how the input data should strcutured in order to run the scoring functions:
data(TestDatInput) colnames(TestDataInput) [1] "idRun" "idBait" "idPrey" "countPrey" "lenPrey" idRun idBait idPrey countPrey lenPrey Unique ID of one AP-MS run Bait ID Prey ID Prey peptide count Protein sequence length of the prey In case of duplcates, a suffix or prefix of e.
The Renal Gene Expression Database (RGED) is online. Number of samples colleceted in the database reached around ~10,000, including DNA microarray and RNA-seq experiments.
Just go ahead to this URL: http://rged.wall-eva.net/