Files in pRoloc

A unifying bioinformatics framework for spatial proteomics

NEWS.md

NAMESPACE

DESCRIPTION

build/vignette.rds

src/Makevars.win

src/RcppExports.cpp

src/pRoloc.cpp

src/Makevars

src/dmvtCpp.cpp

data/dunkley2006params.rda

data/andy2011params.rda

R/machinelearning-functions-tagm-mcmc-helper.R R/machinelearning-functions-ksvm.R R/goannotations.R R/makeGoSet.R R/qsep.R R/go.R R/perTurbo-algorithm.R R/machinelearning-functions-knn.R R/clusterdist-framework.R R/plotting2.R R/plotting3.R R/machinelearning-functions-PerTurbo.R R/machinelearning-functions-rf.R R/clustering-kmeans.R R/AllGenerics.R R/lopims.R R/markers.R R/RcppExports.R R/utils.R R/environment.R R/goenv.R R/machinelearning-functions-nnet.R R/clustering-framework.R R/plottingBayes.R R/machinelearning-framework-map.R R/MLInterfaces.R R/machinelearning-functions-tagm-mcmc.R R/machinelearning-functions-plsda.R R/plotting.R R/zzz.R R/machinelearning-framework-mcmc.R R/hclust.R R/machinelearning-framework.R R/vis.R R/distances.R R/machinelearning-utils.R R/pRolocmarkers.R R/machinelearning-framework-theta.R R/belief.R R/dynamics.R R/phenodisco.R R/MartInterface.R R/machinelearning-functions-nb.R R/MSnSet.R R/machinelearning-functions-tagm-map.R R/chi2.R R/clusterdist-functions.R R/machinelearning-functions-knntl.R R/annotation.R R/machinelearning-functions-svm.R R/plotting-ellipse.R vignettes/v01-pRoloc-tutorial.Rmd

vignettes/pRoloc.bib

vignettes/v05-pRoloc-transfer-learning.Rmd vignettes/v02-pRoloc-ml.Rmd vignettes/v04-pRoloc-goannotations.Rmd vignettes/v03-pRoloc-bayesian.Rmd

vignettes/Figures/mcmc-vis2-1.png

vignettes/Figures/plot3D.png

vignettes/Figures/mcmc-outlier-2.png

vignettes/Figures/mcmc-gg2-1.png

vignettes/Figures/tsne.pdf

vignettes/Figures/tsne.png

vignettes/Figures/Screenshot_PCA2.png

vignettes/Figures/ap12.png

vignettes/Figures/msnset.png

vignettes/Figures/organelle_proteomics.ditaa

vignettes/Figures/ap1.png

vignettes/Figures/organelle_proteomics.png

vignettes/Figures/msnset.ditaa

vignettes/Figures/knnboundaries.R

vignettes/Figures/mcmc-outlier-1.png

vignettes/Figures/mcmc-vis-1.png

vignettes/Figures/bubble-andy.png

vignettes/Figures/ISL-2_16.png

vignettes/Figures/phenodisco.tex

vignettes/Figures/mcmc-outlier-3.png

vignettes/Figures/phenodisco.png

vignettes/Figures/ISL-2_17.png

vignettes/Figures/mcmc-outlier-4.png

vignettes/Figures/F1boxplots.png

vignettes/Figures/ap2.png

vignettes/Figures/knnboundaries.png

man/fDataToUnknown.Rd man/getStockcol.Rd man/ksvmClassification.Rd man/markers.Rd man/plot2Ds.Rd man/QSep-class.Rd man/sampleMSnSet.Rd man/addLegend.Rd man/thetas.Rd man/mcmc-helpers.Rd man/makeGoSet.Rd man/knntlClassification.Rd man/goIdToTerm.Rd man/undocumented.Rd man/checkFvarOverlap.Rd man/defunct.Rd man/addGoAnnotations.Rd man/mrkHClust.Rd man/tagm-mcmc.Rd man/phenoDisco.Rd man/rfOptimisation.Rd man/knntlOptimisation.Rd man/nbOptimisation.Rd man/AnnotationParams-class.Rd man/filterZeroCols.Rd man/highlightOnPlot.Rd man/subsetMarkers.Rd man/nbClassification.Rd man/minMarkers.Rd man/getNormDist.Rd man/perTurboClassification.Rd man/knnClassification.Rd man/plsdaOptimisation.Rd man/mixing_posterior_check.Rd man/filterBinMSnSet.Rd man/filterMaxMarkers.Rd man/plot2D.Rd man/rfClassification.Rd man/getPredictions.Rd man/showGOEvidenceCodes.Rd man/markerMSnSet.Rd man/testMarkers.Rd man/plotEllipse.Rd man/pRolocmarkers.Rd man/getMarkers.Rd man/GenRegRes-class.Rd man/svmClassification.Rd man/checkFeatureNamesOverlap.Rd man/mrkConsProfiles.Rd man/nnetOptimisation.Rd man/getGOFromFeatures.Rd man/MLearn-methods.Rd man/nndist-methods.Rd man/testMSnSet.Rd man/zerosInBinMSnSet.Rd man/chi2-methods.Rd man/filterMinMarkers.Rd man/ksvmOptimisation.Rd man/plotDist.Rd man/plsdaClassification.Rd man/MartInstance-class.Rd man/perTurboOptimisation.Rd man/SpatProtVis-class.Rd man/nnetClassification.Rd man/nicheMeans2D.Rd man/svmOptimisation.Rd man/orderGoAnnotations.Rd man/clustDist.Rd man/classWeights.Rd man/move2Ds.Rd man/addMarkers.Rd man/plotConsProfiles.Rd man/orgQuants.Rd man/MCMCParams.Rd man/empPvalues.Rd man/knnOptimisation.Rd man/lopims.Rd man/spatial2D.Rd man/getMarkerClasses.Rd man/ClustDistList-class.Rd man/ClustDist-class.Rd man/tagm-map.Rd tests/testthat.R tests/testthat/test_ml.R tests/testthat/test_plot2D.R tests/testthat/test_markers.R tests/testthat/test_annotation.R tests/testthat/test_theta.R tests/testthat/test_data.R tests/testthat/test_utils.R tests/testthat/test_qsep.R tests/testthat/test_classWeights.R tests/testthat/test_go.R tests/testthat/test_goannotations.R tests/testthat/test_dist.R tests/testthat/test_tagm_map.R tests/testthat/test_tagm_mcmc.R tests/testthat/test_SpatProtVis.R

inst/CITATION

inst/doc/v01-pRoloc-tutorial.html

inst/doc/v03-pRoloc-bayesian.R inst/doc/v04-pRoloc-goannotations.R inst/doc/v02-pRoloc-ml.R inst/doc/v01-pRoloc-tutorial.Rmd inst/doc/v05-pRoloc-transfer-learning.R

inst/doc/v02-pRoloc-ml.html

inst/doc/v05-pRoloc-transfer-learning.Rmd inst/doc/v02-pRoloc-ml.Rmd inst/doc/v04-pRoloc-goannotations.Rmd

inst/doc/v04-pRoloc-goannotations.html

inst/doc/v05-pRoloc-transfer-learning.html

inst/doc/v03-pRoloc-bayesian.Rmd

inst/doc/v03-pRoloc-bayesian.html

inst/doc/v01-pRoloc-tutorial.R

inst/extdata/marker_dmel.rds

inst/extdata/marker_ggal.rds

inst/extdata/marker_scer_uniprot.rds

inst/extdata/marker_atha.rds

inst/extdata/mil.rds

inst/extdata/dunkley2006pdunittest2.rda

inst/extdata/marker_scer_sgd.rds

inst/extdata/marker_hsap.rds

inst/extdata/params2.rda

inst/extdata/dunkley2006pdunittest_20140408.rda

inst/extdata/marker_mmus.rds

inst/extdata/params.rda

inst/extdata/pdres.rda

inst/extdata/dunkley2006pdunittest1.rda

inst/extdoc/mcmc.md inst/extdoc/mcmc.Rmd inst/scripts/test_pd.R inst/scripts/biomart.R inst/scripts/dynamics.R

inst/figs/plot2D-null-black.png

inst/figs/plot2D-scree.png

inst/figs/plot2D.png

inst/figs/plot2D-null.png

inst/figs/plot2D-null-pch.png

inst/figs/plot2D-null-pch-black.png

inst/figs/plot2D-null-cex.png

inst/figs/plot2D-lda.png

inst/figs/plot2D-hexbin.png

pRoloc documentation built on Nov. 8, 2020, 6:26 p.m.