Man pages for NMikolajewicz/scMiko
scRNAseq analysis functions. Developed using Seurat framework.
| addLogEntry | Add entry to analysis log |
| AddSModuleScore | Calculate standardized module scores for feature expression... |
| aggGroupExpression | Get summary of group expression in Seurat object |
| annotationCloud | Word cloud visualization of cell-type annotations from the... |
| autoPointSize | Automatically determine optimal point size for geom_point() |
| avgGroupExpression | Get summary of group expression in Seurat object |
| baderPathways | Pathway annotations from Bader Lab |
| balanceMatrixSize | Balance matrix dimensions |
| balanceSamples | Subsample cells in seurat object to be balanced... |
| barcodeLabels | Subset and assign labels to seurat |
| benchmarkCluster | Examine cluster-specific scoring performance for... |
| benchmarkScores | Benchmark Miko scoring pipeline using cluster-specific... |
| categoricalColPal | Generate categorical ColorBrewer palette. |
| checkGeneRep | Check gene representation |
| citationCheck | Check pubmed citations for genes |
| cleanCluster | Clean clusters |
| cleanFilterGenes | Clean and filter gene list |
| clearGlobalEnv | Remove variables from global environment |
| clusterFilter | Filter seurat object by specified cluster ids |
| cluster.UMAP | UMAP stratified by cluster ID |
| coherentFraction | Calculate coherent fraction for feature expression program. |
| col2rowname | Assign column entries in data.frame to row names. |
| consolidateNMF | Consolidate several NMF reduction objects into single NMF... |
| da_DEG | Identify correlated genes/pathways associated with... |
| da_Run | Run differential abundance analysis. |
| detectSpecies | Determine species based on gene representation |
| dist2hclust | Hierarchially-cluster distance matrix |
| downsampleSeurat | Downsample single cell data |
| eigengene | Compute eigengene |
| ens2sym.so | Convert gene ensemble to symbol in seurat object |
| entrez2sym | Convert entrez id to gene symbol |
| expression.Plot | Violin plot of single cell gene expression |
| exprUMAP | Visualize gene expression on UMAP |
| featureGradient | Visualize feature activity/expression gradient overlaid on... |
| filterSeurat | Apply QC filters to Seurat Object |
| findArtifactGenes | Identify artifact genes |
| findCDIMarkers | Calculate feature co-dependency index |
| findConservedCDIMarkers | Find CDI-derived markers that are conserved across samples |
| findCorMarkers | Calculate spearman correlations between features. |
| findGiniMarkers | Calculate Gini marker specificity |
| findNetworkFeatures | Identify features for gene program discovery. |
| firstup | Uppercase first letter and lowercase rest |
| fixBarcodeLabel | Fix barcode labels |
| flex.asDT | Outputs datatable with print button options |
| flex.multiTabLogs | Generate multi-tab analysis log list for flexdashboard |
| flex.multiTabPlot | Generate multi-tab ggplot handle list for flexdashboard |
| flex.multiTabPlotly | Generate multi-tab list of plotly figures for flexdashboard |
| flex.multiTabTables | Generate multi-tab datatable list for flexdashboard |
| geneRepCurve | Plot relationship showing percentage of cells expressing... |
| geneSets | List of scMiko gene sets |
| geom_split_violin | Split violin plot using ggplot2 |
| getAnnotationPathways | Returns list of annotations for given Entrez gene IDs |
| getClusterCenters | Get cluster centers |
| getConnectivity | Gene connectivity within network. |
| getDEG | Get differentially expressed genes |
| getDensity | Get local density (z) of bivariate relationship (x,y) |
| getExpressedGenes | Identify expressed genes |
| getExpressingCells | Get cells that express query gene |
| getExpressionMatrix | Get expression matrix from Seurat Object |
| getICAGenes | Get significant ICA genes |
| getJaccard | Jaccard Similarity |
| getLoadPath | Return load path |
| getMitoContent | Calculate mitochondrial content |
| getModuleGenes | Get list of module genes |
| getModulePreservation | Determine module preservation between reference and query... |
| getNMFGenes | Returns top module genes from NMF feature loading matrix |
| getNodesEdges | Get nodes and edges from igraph data.frame for visNetwork |
| getOrderedGroups | Get vector of unique ordered group names from Seurat Object |
| getReductionGenes | Get top loaded features for PCA or ICA dimensional reduction. |
| getSoftThreshold | Analysis of scale free topology for soft-threshold |
| getSoftThreshold2 | Analysis of scale free topology for soft-threshold. Modified... |
| getUMAP | Get UMAP data and plot from Seurat object. |
| group2list | Named list of cells grouped by meta feature from Seurat... |
| highlightUMAP | Highlight cells on UMAP plot |
| id2geneset | Get Reactome/GO geneset |
| id2term | Map Reactome/GO ID to term |
| inferSpecies | Infer species from list of Ensemble ids |
| inferState | Infer activation state using Gaussian decomposition |
| initiateLog | Initiate analysis log |
| jaccardSimilarityMatrix | Jaccard Similarity Matrix |
| lintersect | Returns intersection of all list entries. |
| loadCellRanger | Load CellRanger preprocessed data |
| loadMat | Load gene x cell count matrix into seurat object |
| loadMoffat | Load preprocessed data from Moffat lab sciRNA-seq3 pipeline |
| longDF2namedList | Convert long data frame to named list |
| LR.db | Ligand-Receptor Database |
| mergeSeuratList | Merge list of seurat objects |
| miko_heatmap | Function to draw ggplot heatmaps |
| miko_integrate | scRNAseq integration wrapper |
| miko_message | Print message |
| mikoScore | Calculate Miko module scores for feature expression programs |
| miko_volcano | Draw volcano plot to visualize differential expression. |
| multiCluster | Cluster seurat object at several resolutions |
| multiSilhouette | Evaluate silhouette indices of clustered single cell data... |
| multiSpecificity | Evaluate specificity of single-cell markers across several... |
| namedList2longDF | Convert named list to long data.frame |
| namedList2wideDF | Convert named list to wide data.frame |
| neighborPurity | Compute purity of each cell's neighborhood, as defined by KNN... |
| netHG | Construct functional enrichment network |
| nullScore | Null distribution for standardized module scores. |
| optimalBinSize | Identify optimal bin size for AddModuleScore() function |
| optimalDS | Cut clustered tree at varying heights and overlay with... |
| orderedFactor | Sort factor levels in numerical order |
| p2z | Convert p value to z score |
| parCor | Parallelized correlation |
| pcaElbow | Quickly estimate the 'elbow' of a scree plot (PCA) |
| prepGeneList | Prepare gene to ensemble conversion vector |
| prepSeurat | prep Seurat |
| prepSeurat2 | prep Seurat (Extended adaptation of prepSeurat) |
| projectReduction | Project dimensionally-reduced features onto UMAP |
| propVarPCA | Variance explained by each principal component. |
| pruneSSN | Identify and (optionally) prune gene program features in... |
| pseudoReplicates | Create pseudo-replicates, stratified by grouping variable. |
| pseudotimeRF | Identify pseudotime-dependent genes using Random Forest (RF)... |
| QC.scatterPlot | QC scatter plots |
| QC.violinPlot | QC violin plots |
| qNorm | Quantile Normalization of 2 Vectors |
| recodeBarcode | Recode (i.e., relabel) metadata in Seurat object |
| rescaleValues | Rescale values to specified range. |
| rmDuplicateGenes | Remove duplicate genes from Seurat Object |
| rmvCSVprefix | Remove "ï.." prefix that is appended to csv header |
| runAUC | Run AUCell classification |
| runAUGUR | Prioritize cell types involved in a biological process. |
| runBBKNN | Integrate scRNA-seq data using batch-balanced KNN (BBKNN) |
| runGSEA | Run gene-set enrichment analysis (GSEA) |
| runHG | Run hypergeometric gene enrichment analysis. |
| runICA | Run Independent Component Analysis on gene expression |
| runMS | Run Modular Scoring |
| runNMF | Perform non-negative matrix factorization (NMF) |
| runRPCA | Run Robust Prinicipal Component Analysis |
| runScanorama | Integrate scRNA-seq data using Scanorama |
| runSSN | Perform gene program discovery using SNN analysis |
| runWGCNA | run WGCNA analysis on scRNAseq expression matrix |
| saveHTML | Save figure as html |
| savePDF | Save figure as pdf |
| scale_color_miko | Gradient color scale |
| scale_fill_miko | Gradient fill scale |
| scaleFreeNet | Apply scale-free topology transform to shared-nearest... |
| scaleTOM | TOM matrix rescaling prior to computing consensus topological... |
| scExpression.UMAP | Cell-level gene expression projected on UMAP |
| scMikoUpdate | Reinstall scMiko package |
| scNormScale | Normalize and Scale scRNAseq Data |
| scoreGBM | Annotate glioblastoma (GBM) subtype based on Neftel 2019... |
| scoreStem | Calculate stem index |
| searchAnnotations | Search Reactome/GO databases for terms that match query |
| setResolution | Set cluster resolution |
| signatureCoherence | Evaluate signature coherence. |
| sigScore | Calculate Miko score significance |
| sim2adj | Compute adjaceny matrix from similary (correlation) matrix |
| snip | Winsorize values at lower and upper quantiles. |
| sparse2dense | Convert sparse matrix to dense matrix |
| sparse2df | Convert sparse matrix to data.frame |
| speciesConvert | Convert gene symbol representation to Hs or Mm |
| springNet | Generate spring-embedded network from similarity matrix |
| SSNConnectivity | SSN connectivity plot |
| SSNExpression | SSN connectivity plot |
| SSNResolution | Identify optimal cluster resolution of scale-free shared... |
| subsetDimRed | Get dimensional reduction from Seurat Object for subset of... |
| subsetSeurat | Subset Seurat Object |
| summarizeHG | Summarize hypergeometric enrichment results |
| summarizeModules | Summarize SSN, ICA or NMF gene program/module analyses |
| sym2ens | Convert gene symbol to ensembl |
| sym2entrez | Convert gene symbol to entrez |
| term2id | Map Reactome/GO term to ID |
| theme_miko | scMiko Theme |
| ulength | Number of unique values |
| uniqueFeatures | Get unique features from metadata column in seurat object. |
| updateCentralLog | Update central log |
| updateDimNames | Ensure that all dimNames are correctly specified in Seurat... |
| updateGeneSets | Create/update list of gene sets for scMiko package. |
| upset.Plot | Upset plot |
| value2col | Convert values to color gradient |
| varExpPCA | Get optimal number of principal components |
| variableGenes.Plot | Plot variable genes in Seurat Object |
| vd_Formula | Specify model formula for variance decomposition. |
| vd_Inputs | Specify inputs for variance decomposition analysis |
| vd_Run | Perform Variance Decomposition Analysis |
| vd_UMAP | Generate UMAPs with each variance decomposition covariate... |
| wgcna2graphDF | Convert adjacency or TOM matrix to igraph data.frame |
| wideDF2namedList | Convert wide data.frame to named list |
| wnn_Components | Compute network component UMAPs and visualize component... |
| wnn_Run | Run WNN Multi-Modal Integration. |
| z2p | Convert Z score to p value |
