Files in lgatto/pRoloc

A unifying bioinformatics framework for spatial proteomics

CONDUCT.md NEWS.md R/AllGenerics.R R/MLInterfaces.R R/MSnSet.R R/MartInterface.R R/RcppExports.R R/annotation.R R/belief.R R/chi2.R R/clusterdist-framework.R R/clusterdist-functions.R R/clustering-framework.R R/clustering-kmeans.R R/distances.R R/dynamics.R R/environment.R R/go.R R/goannotations.R R/goenv.R R/hclust.R R/machinelearning-framework-map.R R/machinelearning-framework-mcmc.R R/machinelearning-framework-theta.R R/machinelearning-framework.R R/machinelearning-functions-PerTurbo.R R/machinelearning-functions-knn.R R/machinelearning-functions-knntl.R R/machinelearning-functions-ksvm.R R/machinelearning-functions-nb.R R/machinelearning-functions-nnet.R R/machinelearning-functions-plsda.R R/machinelearning-functions-rf.R R/machinelearning-functions-svm.R R/machinelearning-functions-tagm-map.R R/machinelearning-functions-tagm-mcmc-helper.R R/machinelearning-functions-tagm-mcmc.R R/machinelearning-utils.R R/makeGoSet.R R/markers.R R/pRolocmarkers.R R/perTurbo-algorithm.R R/phenodisco.R R/plotting-ellipse.R R/plotting.R R/plotting2.R R/plotting3.R R/plottingBayes.R R/qsep.R R/utils.R R/vis.R R/zzz.R README.md inst/extdoc/mcmc.Rmd inst/extdoc/mcmc.md inst/scripts/biomart.R inst/scripts/dynamics.R inst/scripts/test_pd.R man/AnnotationParams-class.Rd man/ClustDist-class.Rd man/ClustDistList-class.Rd man/GenRegRes-class.Rd man/MCMCParams.Rd man/MLearn-methods.Rd man/MartInstance-class.Rd man/QSep-class.Rd man/SpatProtVis-class.Rd man/addGoAnnotations.Rd man/addLegend.Rd man/addMarkers.Rd man/checkFeatureNamesOverlap.Rd man/checkFvarOverlap.Rd man/chi2-methods.Rd man/classWeights.Rd man/clustDist.Rd man/defunct.Rd man/empPvalues.Rd man/fDataToUnknown.Rd man/filterBinMSnSet.Rd man/filterMaxMarkers.Rd man/filterMinMarkers.Rd man/filterZeroCols.Rd man/getGOFromFeatures.Rd man/getMarkerClasses.Rd man/getMarkers.Rd man/getNormDist.Rd man/getPredictions.Rd man/getStockcol.Rd man/goIdToTerm.Rd man/highlightOnPlot.Rd man/knnClassification.Rd man/knnOptimisation.Rd man/knntlClassification.Rd man/knntlOptimisation.Rd man/ksvmClassification.Rd man/ksvmOptimisation.Rd man/makeGoSet.Rd man/markerMSnSet.Rd man/markers.Rd man/mcmc-helpers.Rd man/minMarkers.Rd man/mixing_posterior_check.Rd man/move2Ds.Rd man/mrkConsProfiles.Rd man/mrkHClust.Rd man/nbClassification.Rd man/nbOptimisation.Rd man/nicheMeans2D.Rd man/nndist-methods.Rd man/nnetClassification.Rd man/nnetOptimisation.Rd man/orderGoAnnotations.Rd man/orgQuants.Rd man/pRolocmarkers.Rd man/perTurboClassification.Rd man/perTurboOptimisation.Rd man/phenoDisco.Rd man/plot2D.Rd man/plot2Ds.Rd man/plotConsProfiles.Rd man/plotDist.Rd man/plotEllipse.Rd man/plsdaClassification.Rd man/plsdaOptimisation.Rd man/rfClassification.Rd man/rfOptimisation.Rd man/sampleMSnSet.Rd man/showGOEvidenceCodes.Rd man/spatial2D.Rd man/subsetMarkers.Rd man/svmClassification.Rd man/svmOptimisation.Rd man/tagm-map.Rd man/tagm-mcmc.Rd man/testMSnSet.Rd man/testMarkers.Rd man/thetas.Rd man/undocumented.Rd man/zerosInBinMSnSet.Rd tests/testthat.R tests/testthat/test_SpatProtVis.R tests/testthat/test_annotation.R tests/testthat/test_classWeights.R tests/testthat/test_data.R tests/testthat/test_dist.R tests/testthat/test_go.R tests/testthat/test_goannotations.R tests/testthat/test_markers.R tests/testthat/test_ml.R tests/testthat/test_plot2D.R tests/testthat/test_qsep.R tests/testthat/test_tagm_map.R tests/testthat/test_tagm_mcmc.R tests/testthat/test_theta.R tests/testthat/test_utils.R vignettes/Figures/knnboundaries.R vignettes/Figures/tsne.pdf vignettes/v01-pRoloc-tutorial.Rmd vignettes/v02-pRoloc-ml.Rmd vignettes/v03-pRoloc-bayesian.Rmd vignettes/v04-pRoloc-goannotations.Rmd vignettes/v05-pRoloc-transfer-learning.Rmd