Files in NMikolajewicz/scMiko
scRNAseq analysis functions. Developed using Seurat framework.

.Rbuildignore

.gitignore

DESCRIPTION

LICENSE

LICENSE.md

NAMESPACE

R/M1_functions.R

R/M23_functions.R

R/PAGA_functions.R

R/analysis_functions.R R/annotation_functions.R R/da_functions.R R/datasets.R R/flex_functions.R R/hg_functions.R R/integration_functions.R R/marker_functions.R R/module_functions.R R/network_functions.R R/plot_functions.R R/preparation_functions.R R/utility_functions.R R/wnn_functions.R README.md

_pkgdown.yml

data/LR.db.rda

data/baderPathways.rda

data/cell_markers_DEG.csv

data/cell_markers_DEG.rds

data/geneSets.rda

docs/404.html

docs/LICENSE-text.html

docs/LICENSE.html

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docs/vignettes/assets/atlas_tm.png

docs/vignettes/assets/atlas_ts.png

docs/vignettes/assets/atlas_tyser2021.png

docs/vignettes/assets/atlas_zeisel2018.png

index.md man/AddSModuleScore.Rd man/LR.db.Rd man/QC.scatterPlot.Rd man/QC.violinPlot.Rd man/SSNConnectivity.Rd man/SSNExpression.Rd man/SSNResolution.Rd man/addLogEntry.Rd man/aggGroupExpression.Rd man/annotationCloud.Rd man/autoPointSize.Rd man/avgGroupExpression.Rd man/baderPathways.Rd man/balanceMatrixSize.Rd man/balanceSamples.Rd man/barcodeLabels.Rd man/benchmarkCluster.Rd man/benchmarkScores.Rd man/categoricalColPal.Rd man/checkGeneRep.Rd man/citationCheck.Rd man/cleanCluster.Rd man/cleanFilterGenes.Rd man/clearGlobalEnv.Rd man/cluster.UMAP.Rd man/clusterFilter.Rd man/coherentFraction.Rd man/col2rowname.Rd man/consolidateNMF.Rd man/da_DEG.Rd man/da_Run.Rd man/detectSpecies.Rd man/dist2hclust.Rd man/downsampleSeurat.Rd man/eigengene.Rd man/ens2sym.so.Rd man/entrez2sym.Rd man/exprUMAP.Rd man/expression.Plot.Rd man/featureGradient.Rd man/filterSeurat.Rd man/findArtifactGenes.Rd man/findCDIMarkers.Rd man/findConservedCDIMarkers.Rd man/findCorMarkers.Rd man/findGiniMarkers.Rd man/findNetworkFeatures.Rd man/firstup.Rd man/fixBarcodeLabel.Rd man/flex.asDT.Rd man/flex.multiTabLogs.Rd man/flex.multiTabPlot.Rd man/flex.multiTabPlotly.Rd man/flex.multiTabTables.Rd man/geneRepCurve.Rd man/geneSets.Rd man/geom_split_violin.Rd man/getAnnotationPathways.Rd man/getClusterCenters.Rd man/getConnectivity.Rd man/getDEG.Rd man/getDensity.Rd man/getExpressedGenes.Rd man/getExpressingCells.Rd man/getExpressionMatrix.Rd man/getICAGenes.Rd man/getJaccard.Rd man/getLoadPath.Rd man/getMitoContent.Rd man/getModuleGenes.Rd man/getModulePreservation.Rd man/getNMFGenes.Rd man/getNodesEdges.Rd man/getOrderedGroups.Rd man/getReductionGenes.Rd man/getSoftThreshold.Rd man/getSoftThreshold2.Rd man/getUMAP.Rd man/group2list.Rd man/highlightUMAP.Rd man/id2geneset.Rd man/id2term.Rd man/inferSpecies.Rd man/inferState.Rd man/initiateLog.Rd man/jaccardSimilarityMatrix.Rd man/lintersect.Rd man/loadCellRanger.Rd man/loadMat.Rd man/loadMoffat.Rd man/longDF2namedList.Rd man/mergeSeuratList.Rd man/mikoScore.Rd man/miko_heatmap.Rd man/miko_integrate.Rd man/miko_message.Rd man/miko_volcano.Rd man/multiCluster.Rd man/multiSilhouette.Rd man/multiSpecificity.Rd man/namedList2longDF.Rd man/namedList2wideDF.Rd man/neighborPurity.Rd man/netHG.Rd man/nullScore.Rd man/optimalBinSize.Rd man/optimalDS.Rd man/orderedFactor.Rd man/p2z.Rd man/parCor.Rd man/pcaElbow.Rd man/prepGeneList.Rd man/prepSeurat.Rd man/prepSeurat2.Rd man/projectReduction.Rd man/propVarPCA.Rd man/pruneSSN.Rd man/pseudoReplicates.Rd man/pseudotimeRF.Rd man/qNorm.Rd man/recodeBarcode.Rd man/rescaleValues.Rd man/rmDuplicateGenes.Rd man/rmvCSVprefix.Rd man/runAUC.Rd man/runAUGUR.Rd man/runBBKNN.Rd man/runGSEA.Rd man/runHG.Rd man/runICA.Rd man/runMS.Rd man/runNMF.Rd man/runRPCA.Rd man/runSSN.Rd man/runScanorama.Rd man/runWGCNA.Rd man/saveHTML.Rd man/savePDF.Rd man/scExpression.UMAP.Rd man/scMikoUpdate.Rd man/scNormScale.Rd man/scaleFreeNet.Rd man/scaleTOM.Rd man/scale_color_miko.Rd man/scale_fill_miko.Rd man/scoreGBM.Rd man/scoreStem.Rd man/searchAnnotations.Rd man/setResolution.Rd man/sigScore.Rd man/signatureCoherence.Rd man/sim2adj.Rd man/snip.Rd man/sparse2dense.Rd man/sparse2df.Rd man/speciesConvert.Rd man/springNet.Rd man/subsetDimRed.Rd man/subsetSeurat.Rd man/summarizeHG.Rd man/summarizeModules.Rd man/sym2ens.Rd man/sym2entrez.Rd man/term2id.Rd man/theme_miko.Rd man/ulength.Rd man/uniqueFeatures.Rd man/updateCentralLog.Rd man/updateDimNames.Rd man/updateGeneSets.Rd man/upset.Plot.Rd man/value2col.Rd man/varExpPCA.Rd man/variableGenes.Plot.Rd man/vd_Formula.Rd man/vd_Inputs.Rd man/vd_Run.Rd man/vd_UMAP.Rd man/wgcna2graphDF.Rd man/wideDF2namedList.Rd man/wnn_Components.Rd man/wnn_Run.Rd man/z2p.Rd

scMiko.Rproj

vignettes/Cell_Annotation.Rmd vignettes/Cluster_Optimization.Rmd vignettes/DEG.Rmd vignettes/Marker_Catalog.Rmd vignettes/Module_Detection.Rmd

vignettes/assets/atlas_cao2019.png

vignettes/assets/atlas_cao2020.png

vignettes/assets/atlas_mannos2021.png

vignettes/assets/atlas_ps2019.png

vignettes/assets/atlas_tm.png

vignettes/assets/atlas_ts.png

vignettes/assets/atlas_tyser2021.png

vignettes/assets/atlas_zeisel2018.png

vignettes/install.Rmd vignettes/scPipeline_analysis_workflows.Rmd vignettes/scPipeline_getting_started.Rmd vignettes/scPipeline_module_overview.Rmd

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.

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NMikolajewicz/scMiko
scRNAseq analysis functions. Developed using Seurat framework.

Files in NMikolajewicz/scMiko
scRNAseq analysis functions. Developed using Seurat framework.

R Package Documentation

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NMikolajewicz/scMiko scRNAseq analysis functions. Developed using Seurat framework.

Files in NMikolajewicz/scMiko scRNAseq analysis functions. Developed using Seurat framework.

R Package Documentation

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We want your feedback!

NMikolajewicz/scMiko
scRNAseq analysis functions. Developed using Seurat framework.

Files in NMikolajewicz/scMiko
scRNAseq analysis functions. Developed using Seurat framework.