B C D E F G K L M N O P R S T misc
bandle-package | An R package for the Bayesian analysis of differential subcellular localisation experiments |
bandle | Differential localisation experiments using the bandle method |
bandleChain-class | Infrastructure to to store and process MCMC results |
bandleChains-class | Infrastructure to to store and process MCMC results |
bandleJoint | Infrastructure to to store and process MCMC results |
bandleJoint-method | Infrastructure to to store and process MCMC results |
bandleParams-class | Infrastructure to to store and process MCMC results |
bandlePredict | Make predictions from a bandle analysis |
bandleProcess | process bandle results |
bandleSummaries-class | Infrastructure to to store and process MCMC results |
bandleSummary-class | Infrastructure to to store and process MCMC results |
besselK | bessel function of the second kind from boost library |
besselK_boost | bessel function of the second kind from boost library |
binomialDiffLocProb | Compute differential localisation probabilities from ms-based experiments using the bandle method |
bootstrapdiffLocprob | Compute differential localisation probabilities from ms-based experiments using the bandle method |
centeredData | bessel function of the second kind from boost library |
centeredDatamatern | bessel function of the second kind from boost library |
chains | Infrastructure to to store and process MCMC results |
comploglike | bessel function of the second kind from boost library |
comploglikelist | bessel function of the second kind from boost library |
componentloglike | bessel function of the second kind from boost library |
covOrganelle | sample allocations, probabilities and compute loglikilihoods |
diffLoc | Differential localisation experiments using the bandle method |
diffLocalisationProb | Compute differential localisation probabilities from ms-based experiments using the bandle method |
dmvtCpp | bessel function of the second kind from boost library |
dmvtInt | bessel function of the second kind from boost library |
EFDR | Compute the expected False Discovery Rate |
fitGP | Fit a Gaussian process to spatial proteomics data |
fitGPmatern | Fit a Gaussian process to spatial proteomics data |
fitGPmaternPC | Fit a Gaussian process to spatial proteomics data |
gpParams-class | Container for GP results |
gradientamatern | bessel function of the second kind from boost library |
gradientGP | Compute GP gradient |
gradientGPcpp | bessel function of the second kind from boost library |
gradientGPcppmatern | bessel function of the second kind from boost library |
gradientGPmatern | Compute GP gradient |
gradientlogprior | Compute GP gradient |
gradientrhomatern | bessel function of the second kind from boost library |
Gumbel | Compute GP gradient |
kldir | Computes the Kullback-Leibler divergence between Polya-Gamma and Dirichlet priors |
kldirpg | Computes the Kullback-Leibler divergence between Polya-Gamma and Dirichlet priors |
LeapfrogGPcpp | bessel function of the second kind from boost library |
LeapfrogGPcppPC | bessel function of the second kind from boost library |
length-method | Infrastructure to to store and process MCMC results |
likelihoodGP | Compute GP gradient |
likelihoodGPcpp | bessel function of the second kind from boost library |
likelihoodGPmatern | Compute GP gradient |
loglikeGPcpp | bessel function of the second kind from boost library |
mahaInt | bessel function of the second kind from boost library |
makeComponent | bessel function of the second kind from boost library |
matern | bessel function of the second kind from boost library |
mcmc_plot_probs | Generate a violin plot showing the probabilitiy of protein localisation to different organelles |
meanOrganelle | Computes Organelle means and variances using markers |
metropolisGP | Compute GP gradient |
metropolisGPmatern | Compute GP gradient |
mrMethod | robust Mahalanobis distance |
nicheParam-class | Infrastructure to to store and process MCMC results |
nicheParams-class | Infrastructure to to store and process MCMC results |
normalisedData | bessel function of the second kind from boost library |
normalisedDatamatern | bessel function of the second kind from boost library |
outlierAllocationProbs | sample allocations, probabilities and compute loglikilihoods |
params | Infrastructure to to store and process MCMC results |
PCrhomvar | Compute GP gradient |
pg_prior | sample allocations, probabilities and compute loglikilihoods |
plotConvergence | Generates a histogram of ranks (a rank plot) for convergence |
plotGPmatern | Fit a Gaussian process to spatial proteomics data |
plotTable | Generates a table for visualising changes in localisation between two conditions/datasets |
plotTranslocations | Generates a chord diagram or alluvial plot for visualising changes in localisation between two conditions/datasets |
posteriorEstimates | Infrastructure to to store and process MCMC results |
posteriorEstimates-method | Infrastructure to to store and process MCMC results |
posteriorGPmatern | Compute GP gradient |
posteriorgradientGPmatern | Compute GP gradient |
prior_pred_dir | Computes the Kullback-Leibler divergence between Polya-Gamma and Dirichlet priors |
prior_pred_pg | Computes the Kullback-Leibler divergence between Polya-Gamma and Dirichlet priors |
proteinAllocation | sample allocations, probabilities and compute loglikilihoods |
rcpp_pgdraw | bessel function of the second kind from boost library |
reprodScore | robust Mahalanobis distance |
robustMahalanobis | robust Mahalanobis distance |
sampleAlloccpp | bessel function of the second kind from boost library |
sampleDirichlet | bessel function of the second kind from boost library |
sampleGPmeancpp | bessel function of the second kind from boost library |
sampleGPmeanmaterncpp | bessel function of the second kind from boost library |
sampleOutlier | sample allocations, probabilities and compute loglikilihoods |
sampleOutliercpp | bessel function of the second kind from boost library |
sample_weights_dir | sample allocations, probabilities and compute loglikilihoods |
sample_weights_pg | sample allocations, probabilities and compute loglikilihoods |
show-method | Infrastructure to to store and process MCMC results |
sim_dynamic | Generate a dynamic spatial proteomics experiment |
spatial2D | Generate a PCA plot with smoothed probability contours |
StatStratum | inherits StatSratum |
summaries | Infrastructure to to store and process MCMC results |
trenchDetcpp | bessel function of the second kind from boost library |
trenchInvcpp | bessel function of the second kind from boost library |
.bandleChain | Infrastructure to to store and process MCMC results |
.bandleChains | Infrastructure to to store and process MCMC results |
.bandleParams | Infrastructure to to store and process MCMC results |
.bandleSummaries | Infrastructure to to store and process MCMC results |
.bandleSummary | Infrastructure to to store and process MCMC results |
.gpParams | Container for GP results |
.nicheParam | Infrastructure to to store and process MCMC results |
.nicheParams | Infrastructure to to store and process MCMC results |
[-method | Infrastructure to to store and process MCMC results |
[[-method | Infrastructure to to store and process MCMC results |