bioconductor-bandle

name	bioconductor-bandle
description	The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data. Experimental methods supported include dynamic LOPIT-DC, hyperLOPIT, Dynamic Organellar Maps, Dynamic PCP. It provides Bioconductor infrastructure to analyse these data.

bandle

Workflows

Standard Workflow

Perform differential subcellular localisation analysis on mass-spectrometry-based spatial proteomics data across two conditions.

library(bandle)
library(pRolocdata)
data("tan2009r1")

# 1. Load User Input and Extract Common Features (simulated here)
tansim <- sim_dynamic(object = tan2009r1, numRep = 6L, numDyn = 100L)
control <- tansim$lopitrep[1:3]
treatment <- tansim$lopitrep[4:


gpParams  lapplytansimlopitrep x fitGPmaternPCx


K  getMarkerClassestansimlopitrep fcol  
dirPrior  diag K  matrix nrow  K ncol  K
predDirPrior  prior_pred_dirobject  tansimlopitrep dirPrior  dirPrior q  


pc_prior  matrix   each  K ncol  
bandleres  bandleobjectCond1  control objectCond2  treatment 
                    numIter   burnin   thin   
                    gpParams  gpParams pcPrior  pc_prior 
                    numChains   dirPrior  dirPrior seed  


calculateGelmanbandleres
plotOutliersbandleres


bandleres_opt  bandleProcessbandleres
xx  bandlePredictcontrol treatment params  bandleres_opt fcol  
res_control  xx
res_treatment  xx