Files in MacoskoLab/liger

Linked Inference of Genomic Experimental Relationships

NEWS.md R/ATAC.R R/DEG_marker.R R/DoubletFinder.R R/GSEA.R R/RcppExports.R R/aaa.R R/archive.R R/cINMF.R R/classConversion.R R/classes.R R/clustering.R R/data.R R/deprecated.R R/dotplot.R R/downsample.R R/embedding.R R/factorMarker.R R/generics.R R/ggplotting.R R/h5Utility.R R/heatmap.R R/import.R R/integration.R R/liger-methods.R R/ligerCommand_relates.R R/ligerDataset-methods.R R/ligerDataset_subclass-methods.R R/mergeObject.R R/optimizeNewParam.R R/preprocess.R R/rliger-package.R R/selectBatchHVG.R R/subsetObject.R R/util.R R/visualization.R README.md cran-comments.md docs/README.md inst/extdata/ligerToH5AD.R man/H5Apply.Rd man/alignFactors.Rd man/as.liger.Rd man/as.ligerDataset.Rd man/bmmc.Rd man/calcARI.Rd man/calcAgreement.Rd man/calcAlignment.Rd man/calcDatasetSpecificity.Rd man/calcNMI.Rd man/calcPurity.Rd man/centroidAlign.Rd man/closeAllH5.Rd man/commandDiff.Rd man/convertOldLiger.Rd man/coordinate.Rd man/createH5LigerDataset.Rd man/createLiger.Rd man/createLigerDataset.Rd man/deg.marker.Rd man/deg.pw.Rd man/dot-complexHeatmapDotPlot.Rd man/dot-ggCellViolin.Rd man/dot-ggScatter.Rd man/dot-ggplotLigerTheme.Rd man/dot-plotHeatmap.Rd man/downsample.Rd man/exportInteractTrack.Rd man/getFactorMarkers.Rd man/getProportionMito.Rd man/importVignetteData.Rd man/imputeKNN.Rd man/is.newLiger.Rd man/isH5Liger.Rd man/liger-DEG.Rd man/liger-class.Rd man/ligerATACDataset-class.Rd man/ligerCommand-class.Rd man/ligerDataset-class.Rd man/ligerMethDataset-class.Rd man/ligerRNADataset-class.Rd man/ligerSpatialDataset-class.Rd man/ligerToSeurat.Rd man/linkGenesAndPeaks.Rd man/louvainCluster-deprecated.Rd man/makeFeatureMatrix.Rd man/makeInteractTrack-deprecated.Rd man/makeRiverplot-deprecated.Rd man/mapCellMeta.Rd man/mergeH5.Rd man/mergeSparseAll.Rd man/modalOf.Rd man/normalize.Rd man/online_iNMF-deprecated.Rd man/optimizeALS-deprecated.Rd man/optimizeNewData.Rd man/optimizeNewK.Rd man/optimizeNewLambda.Rd man/optimizeSubset.Rd man/pbmc.Rd man/pbmcPlot.Rd man/peak.Rd man/plotBarcodeRank.Rd man/plotCellViolin.Rd man/plotClusterFactorDot.Rd man/plotClusterGeneDot.Rd man/plotClusterGeneViolin.Rd man/plotDensityDimRed.Rd man/plotDimRed.Rd man/plotEnhancedVolcano.Rd man/plotGODot.Rd man/plotGeneLoadings.Rd man/plotGroupClusterDimRed.Rd man/plotHeatmap.Rd man/plotMarkerHeatmap.Rd man/plotPairwiseDEGHeatmap.Rd man/plotProportion.Rd man/plotProportionBox.Rd man/plotSankey.Rd man/plotSpatial.Rd man/plotVarFeatures.Rd man/plotViolin.Rd man/plotVolcano.Rd man/quantileAlignSNF.Rd man/quantileNorm.Rd man/quantile_norm-deprecated.Rd man/read10X.Rd man/read10XFiles.Rd man/readLiger.Rd man/readSubset.Rd man/reexports.Rd man/removeMissing.Rd man/restoreH5Liger.Rd man/retrieveCellFeature.Rd man/reverseMethData.Rd man/rliger-deprecated.Rd man/rliger-package.Rd man/runCINMF.Rd man/runCluster.Rd man/runDoubletFinder.Rd man/runGOEnrich.Rd man/runGSEA.Rd man/runGeneralQC.Rd man/runINMF.Rd man/runIntegration.Rd man/runOnlineINMF.Rd man/runTSNE.Rd man/runUINMF.Rd man/runUMAP.Rd man/scaleNotCenter.Rd man/selectBatchHVG.Rd man/selectGenes.Rd man/selectGenesVST.Rd man/sub-liger.Rd man/sub-ligerDataset.Rd man/sub-sub-liger.Rd man/subsetLiger.Rd man/subsetLigerDataset.Rd man/updateLigerObject.Rd man/writeH5.Rd tests/testthat.R tests/testthat/test_downstream.R tests/testthat/test_factorization.R tests/testthat/test_object.R tests/testthat/test_preprocessing.R tests/testthat/test_subset.R tests/testthat/test_visualization.R vignettes/articles/Integrating_multi_scRNA_data.rmd vignettes/articles/Integrating_scRNA_and_scATAC_data.Rmd vignettes/articles/SNAREseq_walkthrough.Rmd vignettes/articles/STARmap_dropviz_vig.Rmd vignettes/articles/UINMF_vignette.Rmd vignettes/articles/benchmark.Rmd vignettes/articles/cross_species_vig.Rmd vignettes/articles/import_data.Rmd vignettes/articles/installation.Rmd vignettes/articles/liger_object.Rmd vignettes/articles/liger_with_seurat.Rmd vignettes/articles/online_iNMF_tutorial.Rmd vignettes/articles/rna_methylation.Rmd vignettes/liger_vignette.Rmd