Man pages for xu-lab/SINCERA
An R implementation of SINCERA pipeline for processing single-cell RNA-seq data.
| batch.analysis | Analyzing batch difference |
| batch.analysis.ISCCD | Analyze the inter-sample correlation and distance |
| batch.analysis.MA | plot the MA plot for two sets of cells |
| batch.analysis.QQ | plot the QQ plot for two sets of cells |
| celltype.enrichment | Perform cell type enrichment |
| celltype.enrichment.initKB | Contruct the knowledge base for cell type enrichment analysis |
| celltype.validation | Performing rank-aggregation based cell type validation using... |
| cluster.assignment | Partition cells into disjoint clusters |
| cluster.diffgenes | Detect cluster specific differentially expressed genes |
| cluster.geneSelection | Selecting genes for cell cluster identification |
| clusterings.compare | Compare and visualze multiple clustering assignments |
| cluster.ordering | Ordering rows or columns according to a specified order |
| cluster.permutation.analysis | Validating clustering results using permutation analysis |
| cluster.permutation.analysis.1 | Permutation Analysis for determining significance of cluster... |
| consensus_maximization | consensus maximization |
| construct | Construct a sincera object |
| copyCellMeta | Add or update a cell meta data using a predefined cell meta... |
| copyGeneMeta | Add or update a gene meta data using a predefined gene meta... |
| doPCA | Perform PCA based dimension reduction |
| doTSNE | Perform tSNE based dimension reduction |
| drivingforce.getLCC | Extract largest connected component (LCC) of the cell group... |
| drivingforce.inferTRN | Inferring significant TF->TF and TF->TG interactions based on... |
| drivingforce.rankTFs | Rank TFs based on their importance to the LCC measured by six... |
| drivingforce.selectTFs | Select candidate TFs for network inference and TF ranking |
| drivingforce.selectTGs | Select candidate TGs for network inference and TF ranking |
| expr.minimum | Set the lower bound of gene expression |
| exprs.common | Identifying group specific common genes |
| exprs.specificity | Per group expression specificity calculation |
| exprs.synthetic.similarity | Calculating the similarity between each gene profile and... |
| exprs.test.statistic.metric | Normalized and smoothened results of group specific... |
| exprs.unique | Identifying group specific unique genes |
| filterContaminatedCells | Detecting and removing potentially contaminated cells |
| filterLowQualityCells | pre-filtering low quality cells |
| GeneStats | Generate gene level global or per group statistics |
| getCellMeta | Get the meta data of cells in a sincera object |
| getCellNum | Get the number of cells in a sincera object |
| getCells | get the names of cells in specified cell groups in a sincera... |
| getCellType | Get the cell types of given cell groups |
| getCellTypeMarkers | Get cell type marker information defined in a sincera object |
| getExpression | get expression matrix from a sincera object |
| getExprQuantiles | Get and plot the quantiles of gene expression per cell |
| getGeneMeta | Get a gene meta data |
| getGeneNum | Get the number of the genes in a sincera object |
| getGenes | Get the names of all genes in a sincera object |
| getGenesForClustering | Get the set of genes used for cell cluster identification |
| getNodesImportance | Calculate the importance of a node in a graph |
| getPCA | Get the PCA results stored in a sincera object |
| hello | Hello, World! |
| network.inference | Inferring first order conditional dependencies between TFs... |
| normalization.log | log transformation |
| normalization.sqrt | square root transformation |
| normalization.trimmed.mean | Trimmed mean normalization |
| normalization.zscore | Performing zscore scaling of gene expression |
| normalization.zscore.1 | Per group zscore normalization of gene expression profiles |
| plotCellTypeEnrichment | Barplot of the cell type enrichment results |
| plotHC | Plot the dendrogram tree of hierarchical clustering |
| plotHeatmap | Plot heatmap |
| plotMarkers | Plot gene expression patterns |
| plotPCASD | Plot the standard deviation of principal components |
| plotRDS | 2D plot of cells in the PCA or tSNE reduced dimensional... |
| prefilterGenes | Pre-filtering genes with low abundancy |
| setCellMeta | Add or update meta data of cells in a sincera object |
| setCellNames | set the names of all cells in a sincera object |
| setCellType | Map cell clusters to cell types |
| setCellTypeMarkers | Add cell type marker information into sincera |
| setExpression | Update expression matrix in a sincera object |
| setGeneMeta | Add or update meta data of genes in a sincera object |
| setGeneNames | Update the gene names in a sincera object |
| setGenesForClustering | Update the set of genes used for cell cluster identification |
| setPCA | Update the PCA results in sincera |
| signature.prediction | Predicting cell type signature |
| signature.prediction.1 | logistic regression based signature prediction and cross... |
| signature.validation | Validating cell type signature using random subsampling mehod |
| sigpred.testing.sets | Constructing group specific testing sets for signature... |
| sigpred.training.sets | Constructing group specific training sets for signature... |
| sincera | The sincera Class |
| specificity.criterion.selection | Determine the threshold for specificity filter based on a set... |
| specificity.thresholdSelection | Selecting a threshold value for specificity |
