Files in andrewGhazi/bayesianMPRA
A Bayesian framework for modelling MPRA data with an informative, annotation based empirical prior
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/informative_bayesian_mpra.R
R/mledistModified.R
README.md
analysis/BayesianAnalysis.R
analysis/MCMCwithSigmaInference.R
analysis/UlirschOptimization.R
analysis/allVarAnalysis.R
analysis/annotation_selection.R
analysis/annovarUlirsch.R
analysis/barcode_effect_model.R
analysis/barcode_parameter_model.R
analysis/bmpra_power_sim.R
analysis/bugFile.bug
analysis/checkControlsInUlirsch.R
analysis/compareToWilcox.R
analysis/compare_informativeBayes_to_Wilcox.R
analysis/computeVariantVariance.R
analysis/copyExistingSoftware.R
analysis/dataAcquisition.R
analysis/depth_adjust_phi.R
analysis/dist_fitting_redo.R
analysis/findBestPredictors.R
analysis/fullPosterior.R
analysis/fully_parameterised_ulirsch.R
analysis/gammaFitTester.R
analysis/generate_luc_sequences.R
analysis/histoneMarkOutputcorrelations.R
analysis/isolated_sampler_run.R
analysis/jagsModel.R
analysis/jointMeans.R
analysis/kNNprior.R
analysis/kNNpriorOutputs.R
analysis/melnikovAnalysis.R
analysis/multivariatePrior.R
analysis/neg_bin_regression.R
analysis/plotCode.R
analysis/poster_histogram_plot.R
analysis/predictor_variable_selection.R
analysis/priorAnimationCode.R
analysis/priorGain.R
analysis/quantify_prior_performance.R
analysis/raw_ulirsch_analysis.R
analysis/regulomeDB.R
analysis/singleNegBinCheck.R
analysis/stanModelInformativePrior.R
analysis/stanModelOnCounts.R
analysis/sumLikelihoodsPrior.R
analysis/tSNEhistoneVisualization.R
analysis/tewheyAnalysis.R
analysis/tewhey_annotation.R
analysis/tewhey_rs_to_chr_pos.R
analysis/tewhey_subset.R
analysis/tmp.R
analysis/ulirschNegBinWithPrior.R
analysis/unstableParameterEstimates.R
analysis/variational_bayes_tests.R
analysis/visualizeVariantDistribution.R
bayesianMPRA.Rproj
data/mpra_model_string.rda
man/bayesian_mpra_analyze.Rd
man/est_sample_params.Rd
man/find_weights.Rd
man/generate_dist_mat.Rd
man/get_snp_TS_samples.Rd
man/quant_norm_parameter.Rd
man/run_sampler.Rd
man/safelyFitNegBin.Rd
src/stan_files/mpra_model.stan
