Files in YosefLab/VISION
Functional interpretation of single cell RNA-seq latent manifolds

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DESCRIPTION
LICENSE
NAMESPACE
NEWS.md R/AllClasses.R R/AllGenerics.R R/AnalysisFunctions.R R/FileIO.R R/Filters.R R/Microclusters.R R/NormalizationMethods.R R/Projections.R R/RcppExports.R R/Server.R R/SigScoreMethods.R R/TreeBasedMethods.R R/Utilities.R R/methods-Cluster.R R/methods-Signature.R R/methods-Trajectory.R R/methods-TrajectoryProjection.R R/methods-Vision.R R/zzz.R README.md
build_whitelist.sh
docs/LICENSE-text.html
docs/VISION_Report_Manual.pdf
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docs/articles/micropooling.html
docs/articles/trajectories.html
docs/articles/web_only/10xData.html
docs/articles/web_only/Seurat.html
docs/articles/web_only/SignatureAutocorrelation.html
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docs/reference/ProjectionData.html
docs/reference/ServerExpression.html
docs/reference/ServerSigProjMatrix.html
docs/reference/Signature.html
docs/reference/Trajectory.html
docs/reference/TrajectoryProjection.html
docs/reference/VISION-class.html
docs/reference/VISION.html
docs/reference/addLatentSpace.html
docs/reference/addProjection-Vision-method.html
docs/reference/addSignatures.html
docs/reference/addTSNE.html
docs/reference/addUMAP.html
docs/reference/analyze-Vision-method.html
docs/reference/analyzeLocalCorrelations.html
docs/reference/analyzeTrajectoryCorrelations.html
docs/reference/annotateLatentComponents.html
docs/reference/applyFilters.html
docs/reference/applyICA.html
docs/reference/applyISOMap.html
docs/reference/applyMicroClustering.html
docs/reference/applyPCA.html
docs/reference/applyPermutationWPCA.html
docs/reference/applyRBFPCA.html
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docs/reference/applySpectralEmbedding.html
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docs/reference/applyWeightedPCA.html
docs/reference/applytSNE10.html
docs/reference/applytSNE30.html
docs/reference/batchSigEval.html
docs/reference/batchSigEvalNorm.html
docs/reference/batchify.html
docs/reference/calcInterEdgeDistMat.html
docs/reference/calcIntraEdgeDistMat.html
docs/reference/calcSignatureScores.html
docs/reference/calcWeights.html
docs/reference/calculatePearsonCorr.html
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docs/reference/colRankNormalization.html
docs/reference/colVarsSp.html
docs/reference/computeKNNWeights-Trajectory-method.html
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docs/reference/computeLatentSpace.html
docs/reference/computeProjectionGenes.html
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docs/reference/coordinatesToJSON.html
docs/reference/createFalseNegativeMap.html
docs/reference/createGeneSignature.html
docs/reference/createTrajectoryMetaData.html
docs/reference/dot-colNormHelper.html
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docs/reference/evalSigGeneImportanceSparse.html
docs/reference/expressionToJSON.html
docs/reference/fbConsistencyScores.html
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docs/reference/filterData.html
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index.Rmd
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man/Cluster.Rd man/NormData.Rd man/ServerExpression.Rd man/ServerSigProjMatrix.Rd man/Signature.Rd man/Trajectory.Rd man/TrajectoryProjection.Rd man/VISION-class.Rd man/VISION.Rd man/addLatentSpace.Rd man/addProjection-Vision-method.Rd man/addSignatures.Rd man/addTSNE.Rd man/addUMAP.Rd man/analyze-Vision-method.Rd man/analyzeLocalCorrelations.Rd man/analyzeTrajectoryCorrelations.Rd man/annotateLatentComponents.Rd man/applyFilters.Rd man/applyICA.Rd man/applyISOMap.Rd man/applyMicroClustering.Rd man/applyPCA.Rd man/applyPermutationWPCA.Rd man/applyRBFPCA.Rd man/applySimplePPT.Rd man/applySpectralEmbedding.Rd man/applyUMAP.Rd man/applytSNE10.Rd man/applytSNE30.Rd man/batchSigEvalNorm.Rd man/batchify.Rd man/calcInterEdgeDistMat.Rd man/calcIntraEdgeDistMat.Rd man/calcSignatureScores.Rd man/calculateTrajectoryDistances.Rd man/clipBottom.Rd man/clusterCells.Rd man/clusterSigScores.Rd man/clusterSignatures.Rd man/colNormalization.Rd man/colRankNormalization.Rd man/colVarsSp.Rd man/computeKNNWeights-Trajectory-method.Rd man/computeKNNWeights-matrix-method.Rd man/computeLatentSpace.Rd man/computeProjectionGenes.Rd man/convertGeneIds.Rd man/coordinatesToJSON.Rd man/createGeneSignature.Rd man/createTrajectoryMetaData.Rd man/dot-colNormHelper.Rd man/evalSigGeneImportance.Rd man/evalSigGeneImportanceSparse.Rd man/fbConsistencyScores.Rd
man/figures/logo.svg
man/filterGenesFano.Rd man/filterGenesNovar.Rd man/filterGenesThreshold.Rd man/find_knn_parallel.Rd man/fitTree.Rd man/geary_sig_v_proj.Rd man/generatePermutationNull.Rd man/generateProjections.Rd man/generateProjectionsInner.Rd man/generateTrajectoryProjections.Rd man/getLatentSpace.Rd man/getLatentTrajectory.Rd man/getMSE.Rd man/getMetaAutocorrelation.Rd man/getMetaDifferential.Rd man/getNormalizedCopy.Rd man/getNormalizedCopySparse.Rd man/getParam.Rd man/getProjections.Rd man/getSelections.Rd man/getSignatureAutocorrelation.Rd man/getSignatureDifferential.Rd man/getSignatureScores.Rd man/hasUnnormalizedData.Rd man/ilog1p.Rd man/innerEvalSignatureBatchNorm.Rd man/launchServer.Rd man/louvainCluster.Rd man/matLog2.Rd man/matrix_chisq.Rd man/matrix_wilcox.Rd man/matrix_wilcox_cpp.Rd man/noNormalization.Rd man/pearsonCorrToJSON.Rd man/poolCells.Rd man/poolMatrixCols.Rd man/poolMatrixCols_Inner.Rd man/poolMatrixRows.Rd man/poolMetaData.Rd man/processSignatures.Rd man/projectOnTree.Rd man/readSignaturesInput.Rd man/read_10x.Rd man/read_10x_h5.Rd man/read_10x_h5_v2.Rd man/read_10x_h5_v3.Rd man/readjust_clusters.Rd man/registerMethods.Rd man/rowAndColNormalization.Rd man/rowNormalization.Rd man/rowVarsSp.Rd man/saveAndViewResults-Vision-method.Rd man/sigConsistencyScores.Rd man/sigProjMatrixToJSON.Rd man/sigScoresToJSON.Rd man/signatureToJSON.Rd man/sigsToSparseMatrix.Rd man/sigsVsProjection_n.Rd man/sigsVsProjection_pcf.Rd man/sigsVsProjection_pcn.Rd man/sqdist.Rd man/translateCellPositions.Rd man/versionCheck.Rd man/viewResults.Rd
pkgdown/_pkgdown.yml
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pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
src/Geary.cpp
src/Makevars
src/RcppExports.cpp
src/Utilities.cpp
tests/testthat.R tests/testthat/test_create_fp_object.R
tests/testthat/test_data/expression_matrix.txt
tests/testthat/test_data/precomputed_sigs.txt
tests/testthat/test_data/published_signatures/h.all.v5.2.symbols.gmt
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tests/testthat/test_data/sigs_w_values.gmt
tests/testthat/test_data/test_sigMatrix.txt
tests/testthat/test_data/tsne10_res.txt
tests/testthat/test_filters.R tests/testthat/test_geary.R tests/testthat/test_matrix_wilcox.R tests/testthat/test_signature_background.R tests/testthat/test_signatures.R vignettes/VISION-vignette.R vignettes/VISION-vignette.Rmd
vignettes/data/bBM.filtered_gene_list.paper.txt.gz
vignettes/data/expression_matrix.txt.gz
vignettes/data/glio_meta.txt.gz
vignettes/data/h.all.v5.2.symbols.gmt
vignettes/data/hemato_counts.csv.gz
vignettes/data/hemato_covariates.txt.gz
vignettes/micropooling.R vignettes/micropooling.Rmd vignettes/trajectories.R vignettes/trajectories.Rmd vignettes/web_only/10xData.Rmd vignettes/web_only/Seurat.Rmd vignettes/web_only/SignatureAutocorrelation.Rmd vignettes/web_only/Signatures.Rmd
vignettes/web_only/cvalue_demo.png
YosefLab/VISION documentation built on Nov. 22, 2019, 9:52 a.m.